diff --git a/gateway/run.py b/gateway/run.py
index 6f043d448..b8df4deca 100644
--- a/gateway/run.py
+++ b/gateway/run.py
@@ -990,7 +990,7 @@ class GatewayRunner:
         # Memory flush before reset: load the old transcript and let a
         # temporary agent save memories before the session is wiped.
         try:
-            old_entry = self.session_store._sessions.get(session_key)
+            old_entry = self.session_store._entries.get(session_key)
             if old_entry:
                 old_history = self.session_store.load_transcript(old_entry.session_id)
                 if old_history:
@@ -1222,9 +1222,9 @@ class GatewayRunner:
         if not last_user_msg:
             return "No previous message to retry."
         
-        # Truncate history to before the last user message
+        # Truncate history to before the last user message and persist
         truncated = history[:last_user_idx]
-        session_entry.conversation_history = truncated
+        self.session_store.rewrite_transcript(session_entry.session_id, truncated)
         
         # Re-send by creating a fake text event with the old message
         retry_event = MessageEvent(
@@ -1256,7 +1256,7 @@ class GatewayRunner:
         
         removed_msg = history[last_user_idx].get("content", "")
         removed_count = len(history) - last_user_idx
-        session_entry.conversation_history = history[:last_user_idx]
+        self.session_store.rewrite_transcript(session_entry.session_id, history[:last_user_idx])
         
         preview = removed_msg[:40] + "..." if len(removed_msg) > 40 else removed_msg
         return f"↩️ Undid {removed_count} message(s).\nRemoved: \"{preview}\""
@@ -1330,7 +1330,7 @@ class GatewayRunner:
                 lambda: tmp_agent._compress_context(msgs, "", approx_tokens=approx_tokens),
             )
 
-            session_entry.conversation_history = compressed
+            self.session_store.rewrite_transcript(session_entry.session_id, compressed)
             new_count = len(compressed)
             new_tokens = estimate_messages_tokens_rough(compressed)
 
diff --git a/gateway/session.py b/gateway/session.py
index 65528cdd8..c93aba24a 100644
--- a/gateway/session.py
+++ b/gateway/session.py
@@ -567,6 +567,34 @@ class SessionStore:
         with open(transcript_path, "a") as f:
             f.write(json.dumps(message, ensure_ascii=False) + "\n")
     
+    def rewrite_transcript(self, session_id: str, messages: List[Dict[str, Any]]) -> None:
+        """Replace the entire transcript for a session with new messages.
+        
+        Used by /retry, /undo, and /compress to persist modified conversation history.
+        Rewrites both SQLite and legacy JSONL storage.
+        """
+        # SQLite: clear old messages and re-insert
+        if self._db:
+            try:
+                self._db.clear_messages(session_id)
+                for msg in messages:
+                    self._db.append_message(
+                        session_id=session_id,
+                        role=msg.get("role", "unknown"),
+                        content=msg.get("content"),
+                        tool_name=msg.get("tool_name"),
+                        tool_calls=msg.get("tool_calls"),
+                        tool_call_id=msg.get("tool_call_id"),
+                    )
+            except Exception as e:
+                logger.debug("Failed to rewrite transcript in DB: %s", e)
+        
+        # JSONL: overwrite the file
+        transcript_path = self.get_transcript_path(session_id)
+        with open(transcript_path, "w") as f:
+            for msg in messages:
+                f.write(json.dumps(msg, ensure_ascii=False) + "\n")
+
     def load_transcript(self, session_id: str) -> List[Dict[str, Any]]:
         """Load all messages from a session's transcript."""
         # Try SQLite first
diff --git a/hermes_state.py b/hermes_state.py
index ebb3f1dd7..1d1f951c0 100644
--- a/hermes_state.py
+++ b/hermes_state.py
@@ -476,6 +476,17 @@ class SessionDB:
             results.append({**session, "messages": messages})
         return results
 
+    def clear_messages(self, session_id: str) -> None:
+        """Delete all messages for a session and reset its counters."""
+        self._conn.execute(
+            "DELETE FROM messages WHERE session_id = ?", (session_id,)
+        )
+        self._conn.execute(
+            "UPDATE sessions SET message_count = 0, tool_call_count = 0 WHERE id = ?",
+            (session_id,),
+        )
+        self._conn.commit()
+
     def delete_session(self, session_id: str) -> bool:
         """Delete a session and all its messages. Returns True if found."""
         cursor = self._conn.execute(