diff --git a/src/cmdforge/gui/widgets/flow_graph.py b/src/cmdforge/gui/widgets/flow_graph.py
index bd733df..6050ece 100644
--- a/src/cmdforge/gui/widgets/flow_graph.py
+++ b/src/cmdforge/gui/widgets/flow_graph.py
@@ -135,6 +135,7 @@ class FlowGraphWidget(QWidget):
         self._input_node = None
         self._output_node = None
         self._step_nodes: List[CmdForgeBaseNode] = []
+        self._rebuilding = False  # Flag to ignore signals during rebuild
 
         self._setup_ui()
 
@@ -215,13 +216,21 @@ class FlowGraphWidget(QWidget):
         if not self._graph:
             return
 
-        # Clear existing nodes
-        self._graph.clear_session()
+        # Set flag to ignore signals during rebuild
+        self._rebuilding = True
+
+        try:
+            # Clear existing nodes
+            self._graph.clear_session()
+        except Exception:
+            pass  # Ignore errors during clear
+
         self._input_node = None
         self._output_node = None
         self._step_nodes = []
 
         if not self._tool:
+            self._rebuilding = False
             return
 
         # Create input node
@@ -294,6 +303,7 @@ class FlowGraphWidget(QWidget):
             node.set_selected(True)
 
         # Use a timer to fit after the widget is fully rendered
+        # Also clears the rebuilding flag after everything settles
         QTimer.singleShot(50, self._fit_and_clear_selection)
 
     def _fit_and_clear_selection(self):
@@ -303,6 +313,9 @@ class FlowGraphWidget(QWidget):
             # Clear selection
             self._graph.clear_selection()
 
+        # Clear rebuilding flag - now safe to handle user interactions
+        self._rebuilding = False
+
     def select_all_nodes(self):
         """Select all nodes in the graph."""
         if not self._graph:
@@ -419,6 +432,10 @@ class FlowGraphWidget(QWidget):
 
     def _on_nodes_deleted(self, nodes):
         """Handle node deletion from the graph."""
+        # Ignore during rebuild
+        if self._rebuilding:
+            return
+
         # Collect step indices of deleted step nodes (not Input/Output nodes)
         deleted_indices = []
         for node in nodes:
@@ -439,6 +456,10 @@ class FlowGraphWidget(QWidget):
         2. The chain reconnects (previous node → next node)
         3. Disconnected node attaches at the end before Output
         """
+        # Ignore during rebuild
+        if self._rebuilding:
+            return
+
         if not self._tool or not self._tool.steps:
             return