Remove object from non-IFC collections after IFC class assignment.

When an object is assigned to an IFC class, it gets added to the appropriate
        IFC container collection. This method removes it from any non-IFC collections
        it was previously in, ensuring the object only appears in its proper IFC
        spatial container.

src/bonsai/bonsai/bim/module/root/operator.py

@@ -222,6 +222,28 @@ class AssignClass(bpy.types.Operator, tool.Ifc.Operator):
         self.props_to_pset = event.alt
         return self.execute(context)
 
+
+    def _cleanup_collections(self, obj: bpy.types.Object) -> None:
+        """Remove object from non-IFC collections after IFC class assignment.
+        
+        When an object is assigned to an IFC class, it gets added to the appropriate
+        IFC container collection. This method removes it from any non-IFC collections
+        it was previously in, ensuring the object only appears in its proper IFC
+        spatial container.
+        
+        Args:
+            obj: The Blender object to clean up
+        """
+        if len(obj.users_collection) <= 1:
+            return
+        
+        # Identify IFC collections (those starting with "Ifc")
+        non_ifc_collections = [c for c in obj.users_collection if not c.name.startswith("Ifc")]
+        
+        # Remove from all non-IFC collections
+        for collection in non_ifc_collections:
+            collection.objects.unlink(obj)
+
     def _execute(self, context):
         ifc_file = tool.Ifc.get()
         props = tool.Root.get_root_props()
@@ -327,6 +349,9 @@ class AssignClass(bpy.types.Operator, tool.Ifc.Operator):
                     predefined_type=predefined_type,
                     should_add_representation=False,
                 )
+
+                self._cleanup_collections(obj)
+
                 ifcopenshell.api.geometry.assign_representation(tool.Ifc.get(), element, representation)
                 bonsai.core.geometry.switch_representation(
                     tool.Ifc, tool.Geometry, obj=obj, representation=representation
@@ -358,6 +383,9 @@ class AssignClass(bpy.types.Operator, tool.Ifc.Operator):
                     context=ifc_context,
                     ifc_representation_class=self.ifc_representation_class,
                 )
+
+                self._cleanup_collections(obj)
+                
                 representation = tool.Geometry.get_active_representation(obj)
                 if representation:
                     tool.Geometry.reload_representation(obj)