diff --git a/graphify/build.py b/graphify/build.py
index dbbf3d2d1..c6491ae8f 100644
--- a/graphify/build.py
+++ b/graphify/build.py
@@ -1564,6 +1564,7 @@ def build(
         combined["input_tokens"] += ext.get("input_tokens", 0)
         combined["output_tokens"] += ext.get("output_tokens", 0)
     _root = str(Path(root).resolve()) if root else None
+    _dedup_collapsed = 0
     if dedup and combined["nodes"]:
         # Numeric ids must be str before dedup, which keys on them and would
         # raise TypeError in _pick_winner's regex search (#2326). build_from_json
@@ -1585,6 +1586,7 @@ def build(
                     n["source_file"] = _norm_source_file(n["source_file"], _root)
                 if "definition_file" in n:
                     n["definition_file"] = _norm_source_file(n["definition_file"], _root)
+        _before_dedup = len(combined["nodes"])
         combined["nodes"], combined["edges"] = deduplicate_entities(
             combined["nodes"], combined["edges"], communities={},
             dedup_llm_backend=dedup_llm_backend, root=_root,
@@ -1593,7 +1595,13 @@ def build(
             hyperedges=combined.get("hyperedges"),
             protected_ids=protected_ids,
         )
-    return build_from_json(combined, directed=directed, root=_root)
+        _dedup_collapsed = _before_dedup - len(combined["nodes"])
+    G = build_from_json(combined, directed=directed, root=_root)
+    # CLI reads this to tell a dedup shrink from a file deletion (#3774).
+    # Popped before to_json so it is not stored in graph.json.
+    if _dedup_collapsed:
+        G.graph["_dedup_collapsed"] = _dedup_collapsed
+    return G
 
 
 def _norm_label(label: str | None) -> str:
@@ -2249,6 +2257,9 @@ def build_merge(
         if orphaned:
             G.remove_nodes_from(orphaned)
             n_nodes += len(orphaned)
+        # CLI uses this to excuse a smaller graph when the loss is a deletion (#3774).
+        # Popped before to_json so it is not stored in graph.json.
+        G.graph["_pruned_node_count"] = n_nodes
 
         # Report only the prune entries that ACTUALLY matched something — not
         # len(prune_sources), which counted every entry as pruned-from even
diff --git a/graphify/cli.py b/graphify/cli.py
index badf8bdea..ab779f4c4 100644
--- a/graphify/cli.py
+++ b/graphify/cli.py
@@ -3361,7 +3361,8 @@ def dispatch_command(cmd: str) -> None:
                 "[--model M] [--mode deep] [--out DIR|--output DIR] [--google-workspace] [--no-cluster] "
                 "[--no-gitignore] [--code-only] [--no-dedup] "
                 "[--max-workers N] [--token-budget N] [--max-concurrency N] "
-                "[--api-timeout S] [--postgres DSN] [--cargo] [--allow-partial] [--timing]",
+                "[--api-timeout S] [--postgres DSN] [--cargo] [--allow-partial] "
+                "[--allow-dedup-shrink] [--timing]",
                 file=sys.stderr,
             )
             sys.exit(1)
@@ -3383,6 +3384,9 @@ def dispatch_command(cmd: str) -> None:
         cli_postgres_dsn: str | None = None
         cli_cargo: bool = False
         cli_allow_partial: bool = False
+        # --allow-dedup-shrink: write a graph that is smaller because dedup
+        # merged nodes. A deleted file does not need this flag (#3774).
+        cli_allow_dedup_shrink: bool = False
         no_cluster = False
         dedup_llm = False
         # --no-dedup: skip entity deduplication entirely. On an incremental
@@ -3511,6 +3515,8 @@ def dispatch_command(cmd: str) -> None:
                 force = True; i += 1
             elif a == "--allow-partial":
                 cli_allow_partial = True; i += 1
+            elif a == "--allow-dedup-shrink":
+                cli_allow_dedup_shrink = True; i += 1
             elif a == "--timing":
                 cli_timing = True; i += 1
             else:
@@ -4676,15 +4682,17 @@ def dispatch_command(cmd: str) -> None:
         _backup(graphify_out)
         _invalidate_file_manifest_for_db_graph()
         # force=True bypasses the #479 shrink guard entirely. A full build
-        # legitimately shrinks (fuzzy dedup collapse, deleted code) so it keeps
-        # force=True — EXCEPT when this run's extraction was incomplete (an
-        # extractor pass crashed or some semantic chunks failed). Then a partial
-        # graph could silently overwrite a good complete one, so fall back to the
-        # shrink guard (force=False) unless the user opts in with --allow-partial.
+        # legitimately shrinks when files were deleted, so a complete run keeps
+        # force=True — EXCEPT:
+        #   * extraction was incomplete (a pass crashed or a chunk came back
+        #     empty). Fall back to the shrink guard unless --allow-partial.
+        #   * dedup merged nodes and the saved graph would shrink by more than
+        #     this run's deletions (#3774). Refuse the write before to_json unless
+        #     --allow-dedup-shrink. --allow-partial does not accept that shrink.
         #
-        # Both write paths are guarded: the clustered path here via to_json's
-        # #479 check, and the `--no-cluster` raw-dump path above via the same
-        # shrink check against the existing file (existing_graph_node_count).
+        # Both write paths are guarded for an incomplete extraction: the clustered
+        # path here via to_json's #479 check, and the `--no-cluster` raw-dump path
+        # above via the same shrink check against the existing file.
         #
         # Trade-off: this reuses to_json's coarse node-count guard, not the
         # source-aware _check_shrink that watch/update use. On an incremental run
@@ -4692,7 +4700,34 @@ def dispatch_command(cmd: str) -> None:
         # failure can therefore be refused here — recoverable by re-running or
         # passing --allow-partial (the good graph is preserved and the manifest
         # is not stamped, so the retry re-extracts).
+        _gattrs = G.graph if hasattr(G, "graph") else {}
+        _dedup_collapsed = int(_gattrs.pop("_dedup_collapsed", 0) or 0)
+        _pruned_nodes = int(_gattrs.pop("_pruned_node_count", 0) or 0)
         _force_write = cli_allow_partial or not _extraction_incomplete
+        _dedup_shrink_counts: tuple[int, int] | None = None
+        if (
+            not _extraction_incomplete
+            and not no_dedup
+            and not cli_allow_dedup_shrink
+            and _dedup_collapsed > 0
+        ):
+            from graphify.export import existing_graph_node_count as _existing_graph_node_count
+            _existing_n = _existing_graph_node_count(graph_json_path)
+            _new_n = G.number_of_nodes()
+            if isinstance(_existing_n, int) and _new_n < _existing_n - _pruned_nodes:
+                _dedup_shrink_counts = (_existing_n, _new_n)
+        if _dedup_shrink_counts is not None:
+            # Refuse before to_json. to_json's own refusal tells the caller to
+            # pass force=True, which is not this flag (#3774).
+            _old_n, _new_n = _dedup_shrink_counts
+            print(
+                "[graphify extract] error: dedup reduced the graph from "
+                f"{_old_n} nodes to {_new_n} nodes. Refusing to overwrite "
+                f"{graph_json_path}. Pass --allow-dedup-shrink to write "
+                "the smaller graph.",
+                file=sys.stderr,
+            )
+            sys.exit(1)
         # Stamp provenance from the ANALYSED repo, not the shell's cwd: without
         # this, to_json's fallback asks `git rev-parse HEAD` in whatever repo the
         # command was invoked from, so `graphify extract <target>` run from
diff --git a/tests/test_dedup_shrink_refuses_force_write.py b/tests/test_dedup_shrink_refuses_force_write.py
new file mode 100644
index 000000000..620d01908
--- /dev/null
+++ b/tests/test_dedup_shrink_refuses_force_write.py
@@ -0,0 +1,161 @@
+"""A complete `graphify extract` must not force-write a shrink that dedup caused (#3774).
+
+A full build sets force=True, and to_json then skips the #479 node-count check.
+Dedup can merge a same-file duplicate and replace graph.json with no message.
+A deleted file is a different shrink: that write still happens.
+`--allow-dedup-shrink` is the only flag that accepts the dedup shrink.
+"""
+from __future__ import annotations
+
+import json
+
+import pytest
+
+import graphify.__main__ as mainmod
+
+
+def _notes(corpus):
+    readme = str(corpus / "README.md")
+    return [
+        {
+            "id": "readme_decisions_a",
+            "label": "Decisions",
+            "file_type": "document",
+            "source_file": readme,
+            "source_location": "L1",
+        },
+        {
+            "id": "readme_decisions_b",
+            "label": "Decisions",
+            "file_type": "document",
+            "source_file": readme,
+            "source_location": "L2",
+        },
+        {
+            "id": "readme_overview",
+            "label": "Overview",
+            "file_type": "document",
+            "source_file": readme,
+            "source_location": "L3",
+        },
+    ]
+
+
+def _write_graph(path, nodes):
+    path.parent.mkdir(parents=True, exist_ok=True)
+    path.write_text(
+        json.dumps({"nodes": nodes, "links": []}),
+        encoding="utf-8",
+    )
+
+
+def _node_ids(path):
+    data = json.loads(path.read_text(encoding="utf-8"))
+    return [n["id"] for n in data["nodes"]]
+
+
+def _corpus(tmp_path):
+    (tmp_path / "README.md").write_text("# Notes\nThe entry point overview.\n", encoding="utf-8")
+    (tmp_path / "GUIDE.md").write_text("# Guide\nHow to use the thing.\n", encoding="utf-8")
+    return tmp_path
+
+
+def _arm(monkeypatch, tmp_path, *, nodes, extra_argv=()):
+    corpus = _corpus(tmp_path)
+    out_dir = tmp_path / "out"
+    graph_path = out_dir / "graphify-out" / "graph.json"
+    _write_graph(graph_path, nodes)
+    monkeypatch.setenv("ANTHROPIC_API_KEY", "sk-test-fake-key")
+
+    def _stub_corpus(paths, **kwargs):
+        on_chunk = kwargs.get("on_chunk_done")
+        if on_chunk:
+            on_chunk(0, 1, {"nodes": [], "edges": [], "hyperedges": []})
+        return {
+            "nodes": nodes,
+            "edges": [],
+            "hyperedges": [],
+            "input_tokens": 10,
+            "output_tokens": 5,
+        }
+
+    monkeypatch.setattr("graphify.llm.extract_corpus_parallel", _stub_corpus)
+    monkeypatch.setattr(mainmod, "_check_skill_version", lambda _: None)
+    monkeypatch.setattr(
+        mainmod.sys, "argv",
+        ["graphify", "extract", str(corpus), "--backend", "claude",
+         "--out", str(out_dir), *extra_argv],
+    )
+    return graph_path
+
+
+def _run():
+    try:
+        mainmod.main()
+    except SystemExit as exc:
+        return exc.code
+    return 0
+
+
+def test_complete_run_refuses_a_same_file_dedup_shrink(monkeypatch, tmp_path, capsys):
+    """Two same-file duplicates plus one keeper. Dedup merges the pair.
+    The file on disk must keep all three nodes."""
+    graph_path = _arm(monkeypatch, tmp_path, nodes=_notes(tmp_path))
+    code = _run()
+    err = capsys.readouterr().err
+    assert code not in (None, 0)
+    assert _node_ids(graph_path) == [
+        "readme_decisions_a",
+        "readme_decisions_b",
+        "readme_overview",
+    ]
+    assert "3" in err and "2" in err
+    assert "--allow-dedup-shrink" in err
+
+
+def test_allow_dedup_shrink_writes_the_smaller_graph(monkeypatch, tmp_path):
+    graph_path = _arm(
+        monkeypatch, tmp_path, nodes=_notes(tmp_path),
+        extra_argv=["--allow-dedup-shrink"],
+    )
+    code = _run()
+    ids = _node_ids(graph_path)
+    assert code in (None, 0)
+    assert len(ids) == 2
+    assert "readme_overview" in ids
+    assert not {"readme_decisions_a", "readme_decisions_b"} <= set(ids)
+    raw = graph_path.read_text(encoding="utf-8")
+    assert "_dedup_collapsed" not in raw
+    assert "_pruned_node_count" not in raw
+
+
+def test_a_deleted_file_still_writes(monkeypatch, tmp_path):
+    """The shrink is one missing file. Dedup merges nothing. The write proceeds."""
+    corpus = tmp_path
+    readme = str(corpus / "README.md")
+    gone = str(corpus / "gone.md")
+    nodes = [
+        {
+            "id": "readme_overview",
+            "label": "Overview",
+            "file_type": "document",
+            "source_file": readme,
+            "source_location": "L1",
+        },
+        {
+            "id": "gone_notes",
+            "label": "Gone notes",
+            "file_type": "document",
+            "source_file": gone,
+            "source_location": "L1",
+        },
+    ]
+    fresh = [nodes[0]]
+    graph_path = _arm(monkeypatch, tmp_path, nodes=fresh)
+    # Replace the seeded graph with both files. The stub still returns only README.
+    _write_graph(graph_path, nodes)
+    code = _run()
+    ids = _node_ids(graph_path)
+    assert code in (None, 0)
+    assert "gone_notes" not in ids
+    assert "readme_overview" in ids
diff --git a/tests/test_hollow_chunks_arm_shrink_guard.py b/tests/test_hollow_chunks_arm_shrink_guard.py
index 01d6c2082..943a7f5d1 100644
--- a/tests/test_hollow_chunks_arm_shrink_guard.py
+++ b/tests/test_hollow_chunks_arm_shrink_guard.py
@@ -97,8 +97,8 @@ def test_allow_partial_still_overrides(monkeypatch, tmp_path):
 
 
 def test_a_run_with_every_file_covered_keeps_force_write(monkeypatch, tmp_path, capsys):
-    """The ordinary complete run is unchanged: a full build legitimately
-    shrinks (dedup, deleted code) and keeps bypassing the guard."""
+    """A complete run that did not shrink the graph via dedup still force-writes.
+    A dedup shrink is refused unless --allow-dedup-shrink (#3774)."""
     rec = _record_force(monkeypatch)
     _arm(monkeypatch, tmp_path)
     _run()
diff --git a/tests/test_incomplete_build_guard.py b/tests/test_incomplete_build_guard.py
index ced50bc3f..af9bbb2cc 100644
--- a/tests/test_incomplete_build_guard.py
+++ b/tests/test_incomplete_build_guard.py
@@ -100,8 +100,9 @@ def test_allow_partial_forces_write_despite_incomplete(monkeypatch, tmp_path):
 
 
 def test_complete_extraction_keeps_force_write(monkeypatch, tmp_path):
-    # All chunks succeeded -> a complete build legitimately keeps force=True so a
-    # genuine dedup/deletion shrink still overwrites.
+    # All chunks succeeded and dedup did not shrink the saved graph. A complete
+    # run still force-writes in that case. A dedup shrink is refused unless
+    # --allow-dedup-shrink (#3774); see test_dedup_shrink_refuses_force_write.
     rec = _seed_to_json_recorder(monkeypatch, returns=True)
     _arm_extract(monkeypatch, tmp_path, chunk_total=1, chunk_succeeded=1)