diff --git a/pr_agent/tools/pr_code_suggestions.py b/pr_agent/tools/pr_code_suggestions.py
index 0fdc8019fe..5fbee9f202 100644
--- a/pr_agent/tools/pr_code_suggestions.py
+++ b/pr_agent/tools/pr_code_suggestions.py
@@ -333,12 +333,16 @@ def _extract_link(comment_text: str):
                             pr_comment_updated += f"{prev_suggestion_table}\n"
 
                         get_logger().info(f"Persistent mode - updating comment {comment_url} to latest {name} message")
-                        if progress_response:  # publish to 'progress_response' comment, because it refreshes immediately
-                            git_provider.edit_comment(progress_response, pr_comment_updated)
-                            git_provider.remove_comment(comment)
-                            comment = progress_response
-                        else:
-                            git_provider.edit_comment(comment, pr_comment_updated)
+                        git_provider.edit_comment(comment, pr_comment_updated)
+                        if progress_response:
+                            # best-effort: propagating would re-trigger the duplicate-thread fallback below
+                            try:
+                                git_provider.edit_comment(progress_response, "Code suggestions published in the persistent thread above.")
+                                git_provider.remove_comment(progress_response)
+                            except Exception as cleanup_error:
+                                get_logger().warning(
+                                    f"Failed to clean up progress note after persistent update, leaving it in place: {cleanup_error}"
+                                )
                         return comment
             except Exception as e:
                 get_logger().exception(f"Failed to update persistent review, error: {e}")
diff --git a/tests/unittest/test_pr_code_suggestions_core.py b/tests/unittest/test_pr_code_suggestions_core.py
index 0522c1fb9f..1a20a9f74c 100644
--- a/tests/unittest/test_pr_code_suggestions_core.py
+++ b/tests/unittest/test_pr_code_suggestions_core.py
@@ -180,3 +180,30 @@ async def test_push_inline_code_suggestions_falls_back_to_individual_publish_cal
     assert second_retry[0]["relevant_lines_start"] == 2
     assert second_retry[0]["relevant_lines_end"] == 2
     assert "```suggestion\n    return new_worker()" in second_retry[0]["body"]
+
+
+def test_persistent_update_survives_progress_cleanup_failure():
+    """A failing progress-note cleanup must not abort the persistent update:
+    if the cleanup error propagated, the caller would fall back to publishing
+    a new suggestions thread, re-creating the duplicate-thread bug."""
+    initial_header = "## PR Code Suggestions"
+    existing = MagicMock()
+    existing.body = f"{initial_header}\n<!-- aaa1111 -->\n<table>old suggestions</table>"
+    provider = MagicMock()
+    provider.get_issue_comments.return_value = [existing]
+    provider.get_comment_url.return_value = "https://example.test/comment/1"
+    provider.get_latest_commit_url.return_value = "https://example.test/commit/deadbee"
+    # First edit updates the persistent comment and succeeds; the second edit
+    # (re-labelling the progress note before deletion) fails.
+    provider.edit_comment.side_effect = [None, RuntimeError("cleanup failed")]
+    progress_note = MagicMock()
+
+    result = PRCodeSuggestions.publish_persistent_comment_with_history(
+        provider, f"{initial_header}\n<table>new suggestions</table>", initial_header,
+        update_header=False, name="suggestions", final_update_message=False,
+        progress_response=progress_note)
+
+    assert result is existing
+    assert provider.edit_comment.call_count == 2
+    provider.remove_comment.assert_not_called()
+    provider.publish_comment.assert_not_called()