diff --git a/agent/conversation_loop.py b/agent/conversation_loop.py
index bcd84a373bb..3a687fe7138 100644
--- a/agent/conversation_loop.py
+++ b/agent/conversation_loop.py
@@ -602,6 +602,14 @@ def run_conversation(
                 repaired_seq,
                 agent.session_id or "-",
             )
+            # Clamp the SessionDB flush cursor after compaction.  If repair
+            # merged or dropped messages, _last_flushed_db_idx may now point
+            # past the new end of `messages`, causing turn-end flush to skip
+            # the assistant/tool chain entirely (#44837).
+            if hasattr(agent, "_last_flushed_db_idx"):
+                agent._last_flushed_db_idx = min(
+                    agent._last_flushed_db_idx, len(messages)
+                )
 
         api_messages = []
         for idx, msg in enumerate(messages):
diff --git a/run_agent.py b/run_agent.py
index 8026a602c68..0be8b1763fa 100644
--- a/run_agent.py
+++ b/run_agent.py
@@ -1560,7 +1560,12 @@ class AIAgent:
             if not self._session_db_created:
                 self._ensure_db_session()
             start_idx = len(conversation_history) if conversation_history else 0
-            flush_from = max(start_idx, self._last_flushed_db_idx)
+            # Guard against the flush cursor overshooting the message list.
+            # This can happen when repair_message_sequence compacts the list
+            # (merging consecutive users, dropping stray tools) after the
+            # cursor was set.  Fall back to start_idx so we don't skip
+            # persisting the assistant/tool chain (#44837).
+            flush_from = max(start_idx, min(self._last_flushed_db_idx, len(messages)))
             for msg in messages[flush_from:]:
                 role = msg.get("role", "unknown")
                 content = msg.get("content")