### Godot version

4.2 beta 2

### System information

Pop Os 22.04 lts 12th Gen Intel® Core™ i7-12700H × 20 NVIDIA RTX A2000 8GB 32.0  ram. Tested on Forward+ and Mobile

### Issue description

When painting a tile that is rotated or flipped, it looses its physics layer as demonstrated in this video:  

https://github.com/godotengine/godot/assets/33091666/c10f7325-838f-4112-b90d-0c3d9797d08f

Even though in the video I showed this only happening with one of the tiles, it happens with both of them as long as you rotate or flip it. 

### Steps to reproduce

1. Create a tilemap and a tileset
2. Create a physics layer and set collision_visibility_mode to force show. 
3. Assign just created physics layer to tiles
4. Paint the tiles and use rotate or flip tool. 

### Minimal reproduction project

[TileTest.zip](https://github.com/godotengine/godot/files/13067412/TileTest.zip)
multiple_polygon_mode = p_multiple_polygon_mode;
}
void GenericTilePolygonEditor::_notification(int p_what) {
	switch (p_what) {
		case NOTIFICATION_ENTER_TREE: {
			if (!get_meta("reparented", false)) {
				button_expand->set_pressed_no_signal(false);
			}
		} break;
		case NOTIFICATION_THEME_CHANGED: {
			button_expand->set_icon(get_editor_theme_icon(SNAME("DistractionFree")));
			button_create->set_icon(get_editor_theme_icon(SNAME("CurveCreate")));
			button_edit->set_icon(get_editor_theme_icon(SNAME("CurveEdit")));
			button_delete->set_icon(get_editor_theme_icon(SNAME("CurveDelete")));
			button_center_view->set_icon(get_editor_theme_icon(SNAME("CenterView")));
			button_advanced_menu->set_icon(get_editor_theme_icon(SNAME("GuiTabMenuHl")));
			button_pixel_snap->get_popup()->set_item_icon(0, get_editor_theme_icon(SNAME("SnapDisable")));
			button_pixel_snap->get_popup()->set_item_icon(1, get_editor_theme_icon(SNAME("Snap")));
			button_pixel_snap->get_popup()->set_item_icon(2, get_editor_theme_icon(SNAME("SnapGrid")));
			button_pixel_snap->set_icon(button_pixel_snap->get_popup()->get_item_icon(current_snap_option));
			PopupMenu *p = button_advanced_menu->get_popup();
			p->set_item_icon(p->get_item_index(ROTATE_RIGHT), get_editor_theme_icon(SNAME("RotateRight")));
			p->set_item_icon(p->get_item_index(ROTATE_LEFT), get_editor_theme_icon(SNAME("RotateLeft")));
			p->set_item_icon(p->get_item_index(FLIP_HORIZONTALLY), get_editor_theme_icon(SNAME("MirrorX")));
			p->set_item_icon(p->get_item_index(FLIP_VERTICALLY), get_editor_theme_icon(SNAME("MirrorY")));
		} break;
	}
}
void GenericTilePolygonEditor::_bind_methods() {