@@ -218,6 +218,18 @@ jobs:
           [ "$code" -eq 2 ] || { echo "::error::expected exit 2 for no-mesh input, got $code"; exit 1; }
           echo "no-mesh exit code = $code (correct)"
 
+      - name: Headless template applies the new modifier after the existing stack (#468)
+        run: |
+          set -euo pipefail
+          # stack.blend: a cube with a live SUBSURF (levels 1). SUBSURF then
+          # TRIANGULATE is 48 tris; the reversed order a non-first
+          # modifier_apply produces is 72.
+          xvfb-run -a "$BLENDER" --background "$RUNNER_TEMP/out/stack.blend" \
+            --python-exit-code 1 --python templates/headless-batch-script-template/script.py -- \
+            --output "$RUNNER_TEMP/out/stack.glb" --apply-modifier TRIANGULATE
+          xvfb-run -a "$BLENDER" --background --python-exit-code 1 --python tests/smoke/check_glb_tris.py -- \
+            "$RUNNER_TEMP/out/stack.glb" 48
+
       - name: Extension template passes Blender's own manifest validator
         run: |
           set -euo pipefail
@@ -256,6 +268,39 @@ jobs:
           [ "$code" -eq 2 ] || { echo "::error::expected exit 2 for missing input, got $code"; exit 1; }
           echo "missing-input exit code = $code (correct)"
 
+      - name: Pipeline template keeps every part of a shared-mesh, parented GLB (#462, #467)
+        run: |
+          set -euo pipefail
+          # Root rotated 90 deg on X, scaled 2x, at z=3; Body plus two wheels
+          # sharing one mesh. lod0 must hold every part (world bbox == source),
+          # grounded on its world minimum Z, with no node rotation or scale.
+          mkdir -p "$RUNNER_TEMP/out/pipeline_parented"
+          xvfb-run -a "$BLENDER" --background --python-exit-code 1 --python tests/smoke/make_pipeline_glb.py -- \
+            "$RUNNER_TEMP/out/parented_src.glb" --parented
+          xvfb-run -a "$BLENDER" --background --python-exit-code 1 --python templates/ai-asset-pipeline-template/pipeline.py -- \
+            --input "$RUNNER_TEMP/out/parented_src.glb" \
+            --outdir "$RUNNER_TEMP/out/pipeline_parented" \
+            --preset unity \
+            --lod-budgets 1024,256,64 \
+            --collider convex
+          xvfb-run -a "$BLENDER" --background --python-exit-code 1 --python tests/smoke/check_pipeline_glb.py -- \
+            "$RUNNER_TEMP/out/parented_src.glb" "$RUNNER_TEMP/out/pipeline_parented/lod0.glb"
+
+      - name: Falsifier - pipeline template rejects a 2 km asset with exit 8
+        run: |
+          set -euo pipefail
+          xvfb-run -a "$BLENDER" --background --python-exit-code 1 --python tests/smoke/make_pipeline_glb.py -- \
+            "$RUNNER_TEMP/out/huge_src.glb" --radius 1000
+          set +e
+          xvfb-run -a "$BLENDER" --background --python-exit-code 1 --python templates/ai-asset-pipeline-template/pipeline.py -- \
+            --input "$RUNNER_TEMP/out/huge_src.glb" \
+            --outdir "$RUNNER_TEMP/out/pipeline" \
+            --preset unity
+          code=$?
+          set -e
+          [ "$code" -eq 8 ] || { echo "::error::expected exit 8 for out-of-range extent, got $code"; exit 1; }
+          echo "out-of-range extent exit code = $code (correct)"
+
       - name: Headless render template runs (exit 0, PNG produced)
         run: |
           set -euo pipefail
 
@@ -307,9 +307,11 @@ def principled(name, color, metallic, roughness):
 
 
 def apply_selected_mesh_transforms():
-    # Same body as snippets/export_preset_unity.py: one operator call for the
+    # Core of snippets/export_preset_unity.py: one operator call for the
     # whole selection. transform_apply acts on selected_editable_objects, so
     # that is the key to override; selected_objects alone does not narrow it.
+    # The snippet's shared-mesh / parent prelude is left out: this scene
+    # builds single-user, unparented meshes.
     meshes = [o for o in bpy.context.selected_objects if o.type == "MESH"]
     if not meshes:
         return
 
@@ -41,11 +41,34 @@ def scene_units_are_meters(scene):
     return abs(units.scale_length - 1.0) < 1e-6
 
 
+def isolate_mesh_data(objs):
+    # glTF instancing imports as several objects sharing one Mesh (users > 1).
+    # transform_apply refuses multi-user data, and origin_to_base() on shared
+    # data moves every other instance. One copy per object; the last user
+    # keeps the original.
+    for obj in objs:
+        if obj.data.users > 1:
+            obj.data = obj.data.copy()
+
+
+def clear_parent_keep_transform(objs):
+    # glTF node trees import meshes under a root empty that is often rotated
+    # or scaled. Applying the child's own rotation leaves the root's in
+    # matrix_world, so local Z is still not world Z.
+    for obj in objs:
+        if obj.parent is not None:
+            world = obj.matrix_world.copy()
+            obj.parent = None
+            obj.matrix_world = world
+    bpy.context.view_layer.update()
+
+
 def rot_scale_is_identity(obj, tol=1e-6):
     # Rotation and scale both: origin_to_base() shifts along local Z, which is
     # world Z only once rotation is applied. A GLB node often carries a
-    # rotation with identity scale.
-    m = obj.matrix_basis.to_3x3()
+    # rotation with identity scale. Read matrix_world, not matrix_basis: a
+    # child of a rotated root has an identity basis.
+    m = obj.matrix_world.to_3x3()
     return all(
         abs(m[i][j] - (1.0 if i == j else 0.0)) < tol
         for i in range(3)
@@ -68,7 +91,8 @@ def apply_transforms(objs):
 
 
 def origin_to_base(obj):
-    # Precondition: rotation and scale applied (local Z == world Z).
+    # Precondition: unparented, rotation and scale applied (local Z == world
+    # Z), and single-user data (isolate_mesh_data), or other instances move.
     mesh = obj.data
     n = len(mesh.vertices)
     flat = [0.0] * (n * 3)
@@ -120,9 +144,14 @@ if not scene_units_are_meters(scene):
     scene.unit_settings.system = "METRIC"
     scene.unit_settings.scale_length = 1.0
 
-apply_transforms([o for o in imported_meshes() if not rot_scale_is_identity(o)])
+meshes = imported_meshes()
+isolate_mesh_data(meshes)
+clear_parent_keep_transform(meshes)
+apply_transforms([o for o in meshes if not rot_scale_is_identity(o)])
 ```
 
+The scene check above only catches a scene someone changed. A fresh or factory scene is always metric at 1.0, so it cannot see a prop written in centimeters as meters. Also check the geometry: after the apply, the largest bounding-box extent of a prop should be within a plausible range (the pipeline template uses 0.01 m to 100 m and exits non-zero outside it).
+
 `export_apply=True` on glTF applies **modifiers**, not object scale. Unapplied object scale lands on the glTF node. Witness: [`examples/unapplied-scale-gltf/`](https://github.com/TMHSDigital/Blender-Developer-Tools/tree/main/examples/unapplied-scale-gltf).
 
 ### 3. Apply transforms
@@ -131,6 +160,11 @@ apply_transforms([o for o in imported_meshes() if not rot_scale_is_identity(o)])
 
 Gate the apply on rotation **and** scale (`rot_scale_is_identity`). Imported glTF nodes often carry a rotation with identity scale; skipping the apply then makes step 4 ground the mesh along its local Z, which moves it in world space (a cube rotated 90° on X at z=5 shifted by −1 in Y and Z).
 
+Two import shapes break a naive apply, and both are ordinary glTF:
+
+- **Shared mesh data.** Instanced nodes import as several objects on one Mesh (`users == 2` after a round trip). `transform_apply` raises `RuntimeError: Cannot apply to a multi user` on both 4.5.11 and 5.2.1. Run `isolate_mesh_data` first. `transform_apply(isolate_users=True)` also exists on both lines (measured on 4.5.11 and 5.2.1), but it only helps the apply. `origin_to_base` rewrites vertices and still needs single-user data.
+- **Parented meshes.** A child of a rotated or scaled root has an identity `matrix_basis`, so a basis check skips it and the root's rotation stays in `matrix_world`. Unparent with the world matrix kept, then test `matrix_world`. Measured with the pipeline template's parented smoke fixture on 4.5.11 and 5.2.1 (a root rotated 90° on X and scaled 2x at z=3). With the unparent step removed, LOD0 exported with its origin at z=3.0 while the geometry's minimum was z=2.0.
+
 ### 4. Set origin
 
 Origin at the lowest Z of the mesh (sit-on-ground) via `foreach_get` / `foreach_set`, not a Python loop on `mesh.vertices`. This works in local space, so run it only after step 3. See [`examples/prop-origin-transform/`](https://github.com/TMHSDigital/Blender-Developer-Tools/tree/main/examples/prop-origin-transform) for origin-to-base plus `matrix_parent_inverse`.
@@ -182,6 +216,7 @@ Draco, selected-only, explicit `export_yup`, and `export_apply=True` so the deci
 5. **`bm.normal_update()` for flipped faces.** Use `recalc_face_normals`.
 6. **Import then `bpy.ops.mesh.*` with no scale check.** Rule `validate-imported-mesh-scale`.
 7. **Export with a live DECIMATE and `export_apply=False`.** The engine gets the dense mesh. Rule `no-unapplied-modifiers-on-export`.
+8. **Assuming one imported object, single-user and unparented.** Picking the largest mesh drops every other part. Applying shared data raises, and testing `matrix_basis` misses a rotated parent. Isolate the data, unparent, apply, then join if the engine wants one asset.
 
 ## Version correctness
 
 
@@ -33,17 +33,27 @@ Before any preset: meters in the scene (`scale_length == 1.0`), identity object
 ```python
 def apply_selected_mesh_transforms():
     # One operator call for the whole selection. transform_apply reads
-    # selected_editable_objects, so that is the key to override; overriding
-    # selected_objects alone does not narrow it.
+    # selected_editable_objects, so that is the key to override. It refuses
+    # shared (glTF-instanced) mesh data, so copy it per object first, and
+    # unparent keeping the world placement, or a rotated root stays on the node.
     meshes = [o for o in bpy.context.selected_objects if o.type == "MESH"]
     if not meshes:
         return
+    for o in meshes:
+        if o.data.users > 1:
+            o.data = o.data.copy()
+        if o.parent is not None:
+            world = o.matrix_world.copy()
+            o.parent = None
+            o.matrix_world = world
     with bpy.context.temp_override(
         object=meshes[0], active_object=meshes[0], selected_editable_objects=meshes
     ):
         bpy.ops.object.transform_apply(location=False, rotation=True, scale=True)
 ```
 
+The two guards are for ordinary imports. Instanced glTF nodes come back as several objects sharing one Mesh, and `transform_apply` then raises `Cannot apply to a multi user` (4.5.11 and 5.2.1). A mesh under a rotated root has an identity `matrix_basis`. Applying it leaves the root's rotation in `matrix_world`, and `use_selection=True` writes that rotation onto the exported node. Copying the data means instances no longer share one mesh. That is the cost of baking transforms into vertices.
+
 `use_selection=True` on every preset. Draco is opt-in on glTF; do not copy `gltf_draco_export.py` wholesale.
 
 ## glTF is the same for every engine
 
@@ -18,11 +18,19 @@
 
 def apply_selected_mesh_transforms():
     # One operator call for the whole selection. transform_apply reads
-    # selected_editable_objects, so that is the key to override; overriding
-    # selected_objects alone does not narrow it.
+    # selected_editable_objects, so that is the key to override. It refuses
+    # shared (glTF-instanced) mesh data, so copy it per object first, and
+    # unparent keeping the world placement, or a rotated root stays on the node.
     meshes = [o for o in bpy.context.selected_objects if o.type == "MESH"]
     if not meshes:
         return
+    for o in meshes:
+        if o.data.users > 1:
+            o.data = o.data.copy()
+        if o.parent is not None:
+            world = o.matrix_world.copy()
+            o.parent = None
+            o.matrix_world = world
     with bpy.context.temp_override(
         object=meshes[0], active_object=meshes[0], selected_editable_objects=meshes
     ):
 
@@ -16,11 +16,19 @@
 
 def apply_selected_mesh_transforms():
     # One operator call for the whole selection. transform_apply reads
-    # selected_editable_objects, so that is the key to override; overriding
-    # selected_objects alone does not narrow it.
+    # selected_editable_objects, so that is the key to override. It refuses
+    # shared (glTF-instanced) mesh data, so copy it per object first, and
+    # unparent keeping the world placement, or a rotated root stays on the node.
     meshes = [o for o in bpy.context.selected_objects if o.type == "MESH"]
     if not meshes:
         return
+    for o in meshes:
+        if o.data.users > 1:
+            o.data = o.data.copy()
+        if o.parent is not None:
+            world = o.matrix_world.copy()
+            o.parent = None
+            o.matrix_world = world
     with bpy.context.temp_override(
         object=meshes[0], active_object=meshes[0], selected_editable_objects=meshes
     ):
 
@@ -19,11 +19,19 @@
 
 def apply_selected_mesh_transforms():
     # One operator call for the whole selection. transform_apply reads
-    # selected_editable_objects, so that is the key to override; overriding
-    # selected_objects alone does not narrow it.
+    # selected_editable_objects, so that is the key to override. It refuses
+    # shared (glTF-instanced) mesh data, so copy it per object first, and
+    # unparent keeping the world placement, or a rotated root stays on the node.
     meshes = [o for o in bpy.context.selected_objects if o.type == "MESH"]
     if not meshes:
         return
+    for o in meshes:
+        if o.data.users > 1:
+            o.data = o.data.copy()
+        if o.parent is not None:
+            world = o.matrix_world.copy()
+            o.parent = None
+            o.matrix_world = world
     with bpy.context.temp_override(
         object=meshes[0], active_object=meshes[0], selected_editable_objects=meshes
     ):
 
@@ -46,13 +46,25 @@ same way for every preset.
 
 1. Parses script-side args after `--`.
 2. Imports the GLB into an empty scene.
-3. Checks scene units (metric meters), applies object rotation/scale,
-   sits the origin on the lowest Z, recalculates face normals, and
-   prints the evaluated triangle count.
-4. Builds an LOD chain from `--lod-budgets`.
-5. Optionally builds a convex hull or AABB box collider.
-6. Exports each LOD (and the collider) under the chosen engine preset.
-7. Returns explicit exit codes so a CI pipeline can detect failures.
+3. Keeps **every** mesh in the file. Shared (instanced) mesh data gets one
+   copy per object, parents are cleared with the world placement kept,
+   rotation and scale are applied, and all parts are joined into one
+   object (`object.join`, which keeps material slots). A body plus
+   separate wheels ships as one asset with the wheels in place; nothing
+   is dropped. Split the parts in your own code before this step if your
+   engine wants them as separate assets.
+4. Checks the joined asset's largest bounding-box extent against
+   0.01 m to 100 m (`MIN_EXTENT_M` / `MAX_EXTENT_M`). A fresh scene is
+   always metric at scale 1.0, so this measures the imported geometry,
+   not the scene settings. A prop written in centimeters as meters
+   fails here instead of shipping 100x too large.
+5. Sits the origin on the lowest world Z, recalculates face normals,
+   and prints the evaluated triangle count.
+6. Builds an LOD chain from `--lod-budgets` and asserts that each LOD's
+   evaluated triangle count is at or under its budget.
+7. Optionally builds a convex hull or AABB box collider.
+8. Exports each LOD (and the collider) under the chosen engine preset.
+9. Returns explicit exit codes so a CI pipeline can detect failures.
 
 Cleanup order follows `ai-mesh-cleanup`. LOD, collider, and export
 helpers are duplicated from the snippets named in `pipeline.py`'s
@@ -74,6 +86,12 @@ as `export-preset-axis` number their own checks independently.
 | 5 | Import produced no mesh |
 | 6 | `outdir` is not a directory, or glTF export failed / wrote no file |
 | 7 | `--collider convex` produced a hull that is not closed (an edge without exactly two faces), e.g. a flat input |
+| 8 | The joined asset's largest extent is outside 0.01 m to 100 m (wrong source units) |
+| 9 | An LOD's evaluated triangle count is over its `--lod-budgets` entry |
+| 12 | `transform_apply` or `object.join` raised `RuntimeError` (for example multi-user data that was not isolated) |
+
+10 and 11 are skipped on purpose. The repo's shared render gates use them
+(framing and asset quality), so a template never reuses them.
 
 ## Expected environment
 
@@ -91,6 +109,14 @@ as `export-preset-axis` number their own checks independently.
 - **Running without `--background`**. The script still works, but
   Blender opens a UI window and stays open after the script finishes.
   Use `--background` for unattended runs.
+- **Instanced and parented glTF nodes**. Two nodes on one mesh import as
+  two objects sharing one Mesh (`users == 2`), and `transform_apply`
+  refuses that data. A mesh under a rotated root has an identity
+  `matrix_basis`, so the rotation lives only in `matrix_world`. The
+  script isolates and unparents before applying. If you remove that
+  step, a shared-mesh input exits 12. A parented input exits 0 but ships
+  with its origin off the ground: on the smoke fixture, z=3.0 against a
+  geometry minimum of z=2.0.
 - **Operators that need a 3D Viewport context**. Some operators only
   work when a `VIEW_3D` area exists. In headless mode, none does.
   Either rewrite using `bpy.data.*`, or fabricate a window+area via