### 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)
BIND_ENUM_CONSTANT(TILE_LAYOUT_DIAMOND_RIGHT);
	BIND_ENUM_CONSTANT(TILE_LAYOUT_DIAMOND_DOWN);
	BIND_ENUM_CONSTANT(TILE_OFFSET_AXIS_HORIZONTAL);
	BIND_ENUM_CONSTANT(TILE_OFFSET_AXIS_VERTICAL);
	BIND_ENUM_CONSTANT(CELL_NEIGHBOR_RIGHT_SIDE);
	BIND_ENUM_CONSTANT(CELL_NEIGHBOR_RIGHT_CORNER);
	BIND_ENUM_CONSTANT(CELL_NEIGHBOR_BOTTOM_RIGHT_SIDE);
	BIND_ENUM_CONSTANT(CELL_NEIGHBOR_BOTTOM_RIGHT_CORNER);
	BIND_ENUM_CONSTANT(CELL_NEIGHBOR_BOTTOM_SIDE);
	BIND_ENUM_CONSTANT(CELL_NEIGHBOR_BOTTOM_CORNER);
	BIND_ENUM_CONSTANT(CELL_NEIGHBOR_BOTTOM_LEFT_SIDE);
	BIND_ENUM_CONSTANT(CELL_NEIGHBOR_BOTTOM_LEFT_CORNER);
	BIND_ENUM_CONSTANT(CELL_NEIGHBOR_LEFT_SIDE);
	BIND_ENUM_CONSTANT(CELL_NEIGHBOR_LEFT_CORNER);
	BIND_ENUM_CONSTANT(CELL_NEIGHBOR_TOP_LEFT_SIDE);
	BIND_ENUM_CONSTANT(CELL_NEIGHBOR_TOP_LEFT_CORNER);
	BIND_ENUM_CONSTANT(CELL_NEIGHBOR_TOP_SIDE);
	BIND_ENUM_CONSTANT(CELL_NEIGHBOR_TOP_CORNER);
	BIND_ENUM_CONSTANT(CELL_NEIGHBOR_TOP_RIGHT_SIDE);
	BIND_ENUM_CONSTANT(CELL_NEIGHBOR_TOP_RIGHT_CORNER);
	BIND_ENUM_CONSTANT(TERRAIN_MODE_MATCH_CORNERS_AND_SIDES);
	BIND_ENUM_CONSTANT(TERRAIN_MODE_MATCH_CORNERS);
	BIND_ENUM_CONSTANT(TERRAIN_MODE_MATCH_SIDES);
}
TileSet::TileSet() {
	
	tile_lines_mesh.instantiate();
	tile_filled_mesh.instantiate();
}
TileSet::~TileSet() {