@@ -227,6 +227,17 @@ async def _run_backend_generation(self, backend_config: BackendConfig):
                 backend_config, doc_generator, update_opts, prev_graph_path, components, leaf_nodes
             )
             if outcome in ("incremental", "no_change"):
+                # The builder wrote the new graph under this checkout's name. Drop graphs
+                # left by earlier checkouts so the next update has exactly one to pick.
+                from codewiki.src.be.updater.graph_store import (
+                    graph_file_path,
+                    prune_superseded_graphs,
+                )
+
+                prune_superseded_graphs(
+                    backend_config.dependency_graph_dir,
+                    keep=graph_file_path(backend_config.dependency_graph_dir, str(self.repo_path)),
+                )
                 return
             # full_fallback / detector_failure: preserve the old docs, rebuild from scratch
             self._move_docs_aside()
 
@@ -36,22 +36,60 @@ def prev_graph_path(dependency_graph_dir: str, repo_path: str) -> str:
     return graph_file_path(dependency_graph_dir, repo_path)[: -len(".json")] + PREV_SUFFIX
 
 
+def list_graph_files(dependency_graph_dir: str) -> list[str]:
+    """All current ``*_dependency_graph.json`` files in the dir (``.prev.json`` excluded)."""
+    if not os.path.isdir(dependency_graph_dir):
+        return []
+    return sorted(
+        os.path.join(dependency_graph_dir, f)
+        for f in os.listdir(dependency_graph_dir)
+        if f.endswith("_dependency_graph.json")
+    )
+
+
 def find_any_graph_file(dependency_graph_dir: str) -> str | None:
-    """Return the single ``*_dependency_graph.json`` in the dir, if there is exactly one.
+    """Return the previous build's graph when it is not under the current repo name.
 
     The repo may have been analysed from a differently named checkout (a git
-    worktree, for example), so the sanitized name is not always the same.
+    worktree per revision, for example), so the sanitized name is not always
+    the same. With exactly one candidate that is the answer. With several
+    (each earlier worktree left its own file) the newest by mtime is taken and
+    the choice is logged; ``prune_superseded_graphs`` keeps this case rare.
     """
-    if not os.path.isdir(dependency_graph_dir):
+    candidates = list_graph_files(dependency_graph_dir)
+    if not candidates:
         return None
-    candidates = [
-        os.path.join(dependency_graph_dir, f)
-        for f in os.listdir(dependency_graph_dir)
-        if f.endswith("_dependency_graph.json")
-    ]
     if len(candidates) == 1:
         return candidates[0]
-    return None
+    newest = max(candidates, key=os.path.getmtime)
+    logger.warning(
+        "Several dependency graphs found in %s; using the newest (%s) as the previous graph. "
+        "Candidates: %s",
+        dependency_graph_dir,
+        os.path.basename(newest),
+        ", ".join(os.path.basename(c) for c in candidates),
+    )
+    return newest
+
+
+def prune_superseded_graphs(dependency_graph_dir: str, keep: str) -> list[str]:
+    """Delete current-graph files other than ``keep`` so the next update finds one graph.
+
+    The previous graph survives as ``*.prev.json``; only stale copies left by
+    earlier checkouts under other names are removed. Returns the removed paths.
+    """
+    removed = []
+    keep_abs = os.path.abspath(keep)
+    for path in list_graph_files(dependency_graph_dir):
+        if os.path.abspath(path) != keep_abs:
+            os.remove(path)
+            removed.append(path)
+    if removed:
+        logger.info(
+            "Removed superseded dependency graph(s): %s",
+            ", ".join(os.path.basename(r) for r in removed),
+        )
+    return removed
 
 
 def snapshot_old_graph(dependency_graph_dir: str, repo_path: str) -> str | None:
 
@@ -0,0 +1,68 @@
+"""Previous-graph lookup when the repo was analysed from differently named checkouts."""
+
+from __future__ import annotations
+
+import json
+import os
+import time
+
+from codewiki.src.be.updater.graph_store import (
+    find_any_graph_file,
+    graph_file_path,
+    prune_superseded_graphs,
+    snapshot_old_graph,
+)
+
+
+def _write_graph(d, name, payload):
+    path = os.path.join(d, f"{name}_dependency_graph.json")
+    with open(path, "w") as f:
+        json.dump(payload, f)
+    return path
+
+
+def test_single_candidate_is_used_whatever_its_name(tmp_path):
+    d = str(tmp_path)
+    old = _write_graph(d, "rq3_svelte_anchor", {"a": 1})
+    assert find_any_graph_file(d) == old
+    prev = snapshot_old_graph(d, "/repos/rq3-svelte-w1")
+    assert prev is not None and prev.endswith("rq3_svelte_w1_dependency_graph.prev.json")
+    assert json.load(open(prev)) == {"a": 1}
+
+
+def test_several_candidates_pick_newest_not_none(tmp_path):
+    d = str(tmp_path)
+    older = _write_graph(d, "rq3_svelte_anchor", {"rev": "anchor"})
+    time.sleep(0.01)
+    newer = _write_graph(d, "rq3_svelte_w1", {"rev": "w1"})
+    os.utime(older, (1, 1))  # make the order unambiguous
+    assert find_any_graph_file(d) == newer
+    prev = snapshot_old_graph(d, "/repos/rq3-svelte-w2")
+    assert json.load(open(prev)) == {"rev": "w1"}
+
+
+def test_prev_snapshots_are_not_candidates(tmp_path):
+    d = str(tmp_path)
+    _write_graph(d, "rq3_svelte_w1", {"rev": "w1"})
+    with open(os.path.join(d, "rq3_svelte_w1_dependency_graph.prev.json"), "w") as f:
+        json.dump({"rev": "anchor"}, f)
+    assert find_any_graph_file(d).endswith("rq3_svelte_w1_dependency_graph.json")
+
+
+def test_prune_keeps_current_and_prev_only(tmp_path):
+    d = str(tmp_path)
+    _write_graph(d, "rq3_svelte_anchor", {})
+    _write_graph(d, "rq3_svelte_w1", {})
+    current = _write_graph(d, "rq3_svelte_w2", {})
+    with open(os.path.join(d, "rq3_svelte_w2_dependency_graph.prev.json"), "w") as f:
+        json.dump({}, f)
+    removed = prune_superseded_graphs(d, keep=graph_file_path(d, "/repos/rq3-svelte-w2"))
+    assert sorted(os.path.basename(r) for r in removed) == [
+        "rq3_svelte_anchor_dependency_graph.json",
+        "rq3_svelte_w1_dependency_graph.json",
+    ]
+    assert sorted(os.listdir(d)) == [
+        "rq3_svelte_w2_dependency_graph.json",
+        "rq3_svelte_w2_dependency_graph.prev.json",
+    ]
+    assert os.path.exists(current)