diff --git a/src/agent_merge_queue/cli.py b/src/agent_merge_queue/cli.py
index 21b6c04..1b6069a 100755
--- a/src/agent_merge_queue/cli.py
+++ b/src/agent_merge_queue/cli.py
@@ -1672,12 +1672,21 @@ def create_integration_pull_request(
         except QueueError as error:
             if "Reference already exists" not in str(error):
                 raise
+            ref = self._json("api", f"repos/{self.repository}/git/ref/heads/{branch}")
+            branch_head = str((ref.get("object") or {}).get("sha") or "")
+            if not branch_head:
+                raise QueueError(f"integration branch {branch} has no readable head")
+        else:
+            branch_head = base_sha
 
         merged_heads: list[str] = []
         conflict: dict[str, Any] | None = None
         for entry in entries:
+            if self.is_ancestor(entry.head_sha, branch_head):
+                merged_heads.append(entry.head_sha)
+                continue
             try:
-                self._json(
+                merged = self._json(
                     "api",
                     "--method",
                     "POST",
@@ -1689,8 +1698,22 @@ def create_integration_pull_request(
                     "-f",
                     f"commit_message=DeployBot batch {batch_id}: PR #{entry.number}",
                 )
+                branch_head = str((merged or {}).get("sha") or branch_head)
                 merged_heads.append(entry.head_sha)
             except QueueError as error:
+                # GitHub returns 204 with an empty body when a concurrent
+                # update makes this merge a no-op. _json cannot decode that
+                # response, so re-read the authoritative branch head and
+                # accept it only when the exact frozen source is now present.
+                if str(error) == "GitHub returned invalid JSON":
+                    ref = self._json(
+                        "api", f"repos/{self.repository}/git/ref/heads/{branch}"
+                    )
+                    current_head = str((ref.get("object") or {}).get("sha") or "")
+                    if current_head and self.is_ancestor(entry.head_sha, current_head):
+                        branch_head = current_head
+                        merged_heads.append(entry.head_sha)
+                        continue
                 conflict = {
                     "number": entry.number,
                     "head_sha": entry.head_sha,
diff --git a/tests/test_cli.py b/tests/test_cli.py
index dabe23a..010de58 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -2426,6 +2426,7 @@ def test_integration_can_require_non_actions_author(self) -> None:
         client.owner = "example"
         client.coordinator_logins = {"trusted"}
         client.base_sha = Mock(return_value="b" * 40)
+        client.is_ancestor = Mock(return_value=False)
         client._json = Mock(
             side_effect=[
                 {},
@@ -2460,6 +2461,7 @@ def test_integration_requires_app_author_to_be_a_coordinator(self) -> None:
         client.owner = "example"
         client.coordinator_logins = {"trusted"}
         client.base_sha = Mock(return_value="b" * 40)
+        client.is_ancestor = Mock(return_value=False)
         client._json = Mock(
             side_effect=[
                 {},
@@ -3619,6 +3621,7 @@ def test_integration_pr_contains_every_frozen_head(self) -> None:
         client.owner = "example"
         client.name = "repo"
         client.base_sha = Mock(return_value="b" * 40)
+        client.is_ancestor = Mock(return_value=False)
         client._json = Mock(
             side_effect=[
                 {},
@@ -3644,6 +3647,13 @@ def test_integration_pr_contains_every_frozen_head(self) -> None:
             if "repos/example/repo/merges" in call.args
         ]
         self.assertEqual(len(merge_calls), 2)
+        self.assertEqual(
+            [call.args for call in client.is_ancestor.call_args_list],
+            [
+                (first.head_sha, "b" * 40),
+                (second.head_sha, "1" * 40),
+            ],
+        )
         self.assertEqual(
             [call.args for call in client.remove_label.call_args_list],
             [
@@ -3670,6 +3680,7 @@ def test_conflicted_integration_keeps_source_intents_discoverable(self) -> None:
         client.owner = "example"
         client.name = "repo"
         client.base_sha = Mock(return_value="b" * 40)
+        client.is_ancestor = Mock(return_value=False)
         client._json = Mock(
             side_effect=[
                 {},
@@ -3830,6 +3841,89 @@ def test_resumed_integration_finishes_source_label_delegation(self) -> None:
             ],
         )
 
+    def test_integration_skips_source_already_contained_transitively(self) -> None:
+        cumulative = entry(1, "shared.py")
+        contained = entry(2, "shared.py")
+        batch = new_batch([cumulative, contained], frozen_at="2026-06-20T00:00:00Z")
+        client = object.__new__(GitHub)
+        client.config = parse_config(
+            {
+                "queue": {
+                    "required_checks": ["CI"],
+                    "trusted_actors": ["trusted"],
+                },
+                "integration": {"mode": "all"},
+            }
+        )
+        client.repository = "example/repo"
+        client.owner = "example"
+        client.name = "repo"
+        client.base_sha = Mock(return_value="b" * 40)
+        client.is_ancestor = Mock(side_effect=[False, True])
+        client._json = Mock(
+            side_effect=[
+                {},
+                {"sha": "m" * 40},
+                [],
+                {"number": 99, "html_url": "https://example.test/99"},
+            ]
+        )
+        client.comment = Mock()
+        client.labels = Mock(return_value={"merge-queue", "deploy-requested"})
+        client.remove_label = Mock()
+
+        result = client.create_integration_pull_request(
+            batch=batch, entries=[cumulative, contained]
+        )
+
+        self.assertIsNone(result["conflict"])
+        merge_calls = [
+            call
+            for call in client._json.call_args_list
+            if "repos/example/repo/merges" in call.args
+        ]
+        self.assertEqual(len(merge_calls), 1)
+        marker = client.comment.call_args.args[1]
+        self.assertIn(cumulative.head_sha, marker)
+        self.assertIn(contained.head_sha, marker)
+
+    def test_integration_recovers_empty_merge_response_after_race(self) -> None:
+        source = entry(1, "shared.py")
+        batch = new_batch([source], frozen_at="2026-06-20T00:00:00Z")
+        client = object.__new__(GitHub)
+        client.config = parse_config(
+            {
+                "queue": {
+                    "required_checks": ["CI"],
+                    "trusted_actors": ["trusted"],
+                },
+                "integration": {"mode": "all"},
+            }
+        )
+        client.repository = "example/repo"
+        client.owner = "example"
+        client.name = "repo"
+        client.base_sha = Mock(return_value="b" * 40)
+        client.is_ancestor = Mock(side_effect=[False, True])
+        client._json = Mock(
+            side_effect=[
+                {},
+                QueueError("GitHub returned invalid JSON"),
+                {"object": {"sha": "m" * 40}},
+                [],
+                {"number": 99, "html_url": "https://example.test/99"},
+            ]
+        )
+        client.comment = Mock()
+        client.labels = Mock(return_value={"merge-queue", "deploy-requested"})
+        client.remove_label = Mock()
+
+        result = client.create_integration_pull_request(batch=batch, entries=[source])
+
+        self.assertIsNone(result["conflict"])
+        marker = client.comment.call_args.args[1]
+        self.assertIn(source.head_sha, marker)
+
     def test_failed_integration_pr_creation_removes_its_orphan_branch(self) -> None:
         first = entry(1, "shared.py")
         second = entry(2, "shared.py")
@@ -3848,6 +3942,7 @@ def test_failed_integration_pr_creation_removes_its_orphan_branch(self) -> None:
         client.owner = "example"
         client.name = "repo"
         client.base_sha = Mock(return_value="b" * 40)
+        client.is_ancestor = Mock(return_value=False)
         client._json = Mock(
             side_effect=[
                 {},