diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2310a1e..86c1d5c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,10 @@
 
 Full release notes with details on each version: [GitHub Releases](https://github.com/safishamsi/graphify/releases)
 
+## Unreleased
+
+- Fix: cross-file `indirect_call` edges were dropped by `graphify extract` on the CLI (a 0.9.4 regression). The callable-target guard for cross-file indirect dispatch was keyed on node ids collected before the id-relativization/disambiguation passes; when the scan root relativizes ids (the CLI's default, `cache_root == project root`), those ids went stale and every cross-file indirect edge was silently dropped — only same-file ones survived. Callable-ness is now read from a node marker that rides through the remaps, so `submit(imported_fn)`, imported dispatch tables, assignment/getattr aliases across files resolve on the CLI as they already did via the `extract()` API.
+
 ## 0.9.4 (2026-07-01)
 
 - Fix: Ruby class inheritance now emits an `inherits` edge (#1535, thanks @Synvoya). `class Dog < Animal` produced `contains`/method/call edges but no `inherits` edge — the inheritance handler had branches for Java/Kotlin/C#/Scala/C++/PHP/Swift/Python but none for Ruby, so the `superclass` field was never read. Handles both bare (`< Animal`) and qualified (`< M::Base`) superclasses.
diff --git a/graphify/extract.py b/graphify/extract.py
index f0a4927..30388c1 100644
--- a/graphify/extract.py
+++ b/graphify/extract.py
@@ -5051,11 +5051,15 @@ def _extract_generic(
 
     result = {"nodes": nodes, "edges": clean_edges, "raw_calls": raw_calls}
     if callable_def_nids:
-        # Function / method / class def ids in this file. The cross-file
-        # indirect_call resolvers use the union of these to ensure a callback
-        # passed by name resolves only to a real callable, never a same-named
-        # data symbol (mirrors the in-file `callable_def_nids` guard).
-        result["callable_nids"] = sorted(callable_def_nids)
+        # Mark function / method / class defs with a `_callable` attribute so the
+        # cross-file indirect_call pass can resolve a by-name callback only to a real
+        # callable (never a same-named data symbol). A marker rides on the node dict
+        # and survives the id-remap / disambiguation passes in extract(); a pre-remap
+        # id set would go stale and silently drop every cross-file indirect edge when
+        # ids are relativized (#1566 regression). Stripped before output, like origin_file.
+        for n in nodes:
+            if n["id"] in callable_def_nids:
+                n["_callable"] = True
     if swift_extensions:
         result["swift_extensions"] = swift_extensions
     if type_table:
@@ -15182,15 +15186,15 @@ def extract(
     all_nodes: list[dict] = []
     all_edges: list[dict] = []
     all_raw_calls: list[dict] = []
-    # Union of every file's function / method / class def ids. The cross-file
-    # indirect_call pass resolves a callback passed by name only to one of these,
-    # so a same-named data symbol can never become an indirect-dispatch target.
-    callable_nids: set[str] = set()
     for result in per_file:
         all_nodes.extend(result.get("nodes", []))
         all_edges.extend(result.get("edges", []))
         all_raw_calls.extend(result.get("raw_calls", []))
-        callable_nids.update(result.get("callable_nids", ()))
+    # Function / method / class def ids for the cross-file indirect_call callable
+    # guard. Built from the `_callable` node marker AFTER the id-remap / disambiguation
+    # passes below (which rewrite node ids), so it can never go stale — see the
+    # marker set in the per-file extractor. Populated just before the pass that uses it.
+    callable_nids: set[str] = set()
 
     _augment_symbol_resolution_edges(paths, all_nodes, all_edges, root)
 
@@ -15373,6 +15377,12 @@ def extract(
             key = normalised.lower()
             global_label_to_nids.setdefault(key, []).append(n["id"])
 
+    # Callable-def ids for the indirect_call callable guard, read from the `_callable`
+    # marker on the FINAL (post-remap) nodes — so a callback resolves only to a real
+    # function/method/class, never a same-named data symbol, and the guard never goes
+    # stale when node ids were relativized/disambiguated above (#1566).
+    callable_nids = {n["id"] for n in all_nodes if n.get("_callable")}
+
     # Build evidence index from import edges so cross-file calls backed by an
     # explicit import statement can be promoted from INFERRED to EXTRACTED.
     # Direct symbol imports (`import { foo }` / `const { foo } = require()`) are
@@ -15557,6 +15567,7 @@ def extract(
     # cache keeps its own copy, which is what the colliding-id pass reads on a cache hit.
     for n in all_nodes:
         n.pop("origin_file", None)
+        n.pop("_callable", None)  # internal indirect_call marker — never ships to graph.json
 
     # Tag AST provenance so the incremental watch rebuild can distinguish
     # AST-extracted nodes from semantic/LLM nodes. On a full re-extraction
diff --git a/tests/test_indirect_dispatch.py b/tests/test_indirect_dispatch.py
index ae2fd63..ee3d36b 100644
--- a/tests/test_indirect_dispatch.py
+++ b/tests/test_indirect_dispatch.py
@@ -201,6 +201,33 @@ def _extract_dir(tmp_path, files: dict[str, str]):
     return r, nid
 
 
+def test_cross_file_indirect_survives_id_relativization(tmp_path):
+    """Regression: when the scan root relativizes node ids (cache_root == project
+    root, as the `graphify extract` CLI passes), the id-remap rewrites node ids
+    AFTER per-file extraction. The cross-file indirect callable guard must read
+    callable-ness from a node marker that survives the remap, not a stale pre-remap
+    id set — otherwise every cross-file indirect_call is silently dropped (only
+    in-file ones survive). This is the exact shape the CLI hit."""
+    base = tmp_path / "proj"
+    (base / "handlers").mkdir(parents=True)
+    (base / "handlers" / "__init__.py").write_text("def on_event(x):\n    return x\n")
+    (base / "scheduler.py").write_text(
+        "from handlers import on_event\n\n\ndef schedule(pool):\n    pool.submit(on_event)\n"
+    )
+    old = os.getcwd()
+    try:
+        os.chdir(base)
+        # cache_root == project root triggers source_file relativization + id-remap
+        r = extract([Path("handlers/__init__.py"), Path("scheduler.py")],
+                    cache_root=base, parallel=False)
+    finally:
+        os.chdir(old)
+    nid = {n["label"].rstrip("()"): n["id"] for n in r["nodes"]}
+    assert (nid["schedule"], nid["on_event"]) in _rels(r, "indirect_call")
+    # the internal callable marker must never ship to graph.json
+    assert not any("_callable" in n for n in r["nodes"])
+
+
 def test_cross_file_imported_callback_emits_indirect_call(tmp_path):
     r, nid = _extract_dir(tmp_path, {
         "handlers.py": "def on_event(x):\n    return x\n",