diff --git a/crates/bevy_scene/src/lib.rs b/crates/bevy_scene/src/lib.rs
index fe15866c14..f7d52e6b62 100644
--- a/crates/bevy_scene/src/lib.rs
+++ b/crates/bevy_scene/src/lib.rs
@@ -81,7 +81,7 @@ impl Plugin for ScenePlugin {
                     if let Some(instance_ids) = scene_spawner.spawned_dynamic_scenes.get_mut(&id) {
                         instance_ids.remove(&scene_instance);
                     }
-                    scene_spawner.despawn_instance(scene_instance);
+                    scene_spawner.unregister_instance(scene_instance);
                 }
             });
 
@@ -95,7 +95,7 @@ impl Plugin for ScenePlugin {
                     let Some(mut scene_spawner) = world.get_resource_mut::<SceneSpawner>() else {
                         return;
                     };
-                    scene_spawner.despawn_instance(scene_instance);
+                    scene_spawner.unregister_instance(scene_instance);
                 }
             });
     }
diff --git a/crates/bevy_scene/src/scene_spawner.rs b/crates/bevy_scene/src/scene_spawner.rs
index 3d4014f123..cf8195e676 100644
--- a/crates/bevy_scene/src/scene_spawner.rs
+++ b/crates/bevy_scene/src/scene_spawner.rs
@@ -179,10 +179,19 @@ impl SceneSpawner {
     }
 
     /// Schedule the despawn of a scene instance, removing all its entities from the world.
+    ///
+    /// Note: this will despawn _all_ entities associated with this instance, including those
+    /// that have been removed from the scene hierarchy. To despawn _only_ entities still in the hierarchy,
+    /// despawn the relevant root entity directly.
     pub fn despawn_instance(&mut self, instance_id: InstanceId) {
         self.instances_to_despawn.push(instance_id);
     }
 
+    /// This will remove all records of this instance, without despawning any entities.
+    pub fn unregister_instance(&mut self, instance_id: InstanceId) {
+        self.spawned_instances.remove(&instance_id);
+    }
+
     /// Immediately despawns all instances of a dynamic scene.
     pub fn despawn_sync(
         &mut self,