diff --git a/CHANGELOG.md b/CHANGELOG.md
index f750348e..d477a85c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,7 @@ Full release notes with details on each version: [GitHub Releases](https://githu
 
 ## 0.9.46 (unreleased)
 
+- Fix: pruning a source file now also sweeps the external-import placeholder nodes it strands at degree 0, instead of leaving them to accumulate in the node count, `GRAPH_REPORT.md`, and exports; genuinely-isolated real nodes (which carry a `source_file`) are never touched (#2807, thanks @abhay-codes07).
 - Fix: when two edges connect the same node pair with different relations, the graph builder now keeps the more specific relation (`calls`, `imports`, `inherits`, ...) instead of letting a generic `references`/`uses`/`mentions` overwrite it; previously a real `calls` could be downgraded to `references` and then dropped from the call graph (#2803, thanks @abhay-codes07).
 
 ## 0.9.45 (2026-08-16)
diff --git a/graphify/build.py b/graphify/build.py
index d2309151..6cae7539 100644
--- a/graphify/build.py
+++ b/graphify/build.py
@@ -1839,6 +1839,12 @@ def build_merge(
         # match on source_file. A node with neither a source_file nor an edge
         # names nothing and connects nothing, so dropping it loses no
         # information (#2807).
+        #
+        # A single pass suffices: external-import stubs are only ever edge
+        # TARGETS (extractors mint them as the target of an imports_from/
+        # references/inherits edge, never as a source), so removing one can
+        # never drop another to degree 0. A future extractor emitting a
+        # stub->stub edge would require iterating this to a fixpoint.
         orphaned = [
             n for n, d in G.nodes(data=True)
             if not d.get("source_file")
diff --git a/tests/test_prune_sweeps_orphans.py b/tests/test_prune_sweeps_orphans.py
index 46c6265f..925f0ffe 100644
--- a/tests/test_prune_sweeps_orphans.py
+++ b/tests/test_prune_sweeps_orphans.py
@@ -153,3 +153,33 @@ def test_a_prune_that_matches_nothing_sweeps_nothing(tmp_path):
 def test_pruning_every_file_leaves_an_empty_graph(tmp_path):
     G = _prune(_corpus_graph(), tmp_path, ["a.py", "b.py"])
     assert G.number_of_nodes() == 0, sorted(G.nodes)
+
+
+def test_sweeping_an_orphan_does_not_trip_the_shrink_guard(tmp_path):
+    """The #479 shrink guard raises on unexplained node loss. Swept orphans are
+    source-less, so they must be treated as explained: build_merge completes
+    (does not raise) and returns the pruned graph with the orphan gone."""
+    # build_merge itself runs the guard; this pruning both a file AND sweeping
+    # its stranded stub must not raise.
+    G = _prune(_corpus_graph(), tmp_path, ["a.py"])
+    assert "mod_a_path" not in G.nodes  # swept orphan
+    assert "mod_b_keep" in G.nodes      # unrelated file survives
+
+
+def test_a_stub_referenced_by_a_surviving_file_is_not_swept(tmp_path):
+    """A stub shared by two files must survive when only one referrer is pruned
+    (single-pass sweep only removes it once it is genuinely degree 0)."""
+    nodes = [
+        {"id": "mod_a_run", "label": "run()", "file_type": "code", "source_file": "a.py"},
+        {"id": "mod_b_run", "label": "run()", "file_type": "code", "source_file": "b.py"},
+        {"id": "ext_path", "label": "Path", "file_type": "code"},  # shared external stub
+    ]
+    edges = [
+        {"source": "mod_a_run", "target": "ext_path", "relation": "references",
+         "confidence": "EXTRACTED", "source_file": "a.py"},
+        {"source": "mod_b_run", "target": "ext_path", "relation": "references",
+         "confidence": "EXTRACTED", "source_file": "b.py"},
+    ]
+    G = _prune(build_from_json(_extraction(nodes, edges)), tmp_path, ["a.py"])
+    assert "ext_path" in G.nodes, "stub still referenced by b.py must not be swept"
+    assert "mod_b_run" in G.nodes