### 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)
};
protected:
	bool _set(const StringName &p_name, const Variant &p_value);
	bool _get(const StringName &p_name, Variant &r_ret) const;
	void _get_property_list(List<PropertyInfo> *p_list) const;
	void _validate_property(PropertyInfo &p_property) const;
private:
	
	
	TileShape tile_shape = TILE_SHAPE_SQUARE;
	TileLayout tile_layout = TILE_LAYOUT_STACKED;
	TileOffsetAxis tile_offset_axis = TILE_OFFSET_AXIS_HORIZONTAL;
	Size2i tile_size = Size2i(16, 16); 
	
	bool uv_clipping = false;
	struct OcclusionLayer {
		uint32_t light_mask = 1;
		bool sdf_collision = false;
	};
	Vector<OcclusionLayer> occlusion_layers;
	Ref<ArrayMesh> tile_lines_mesh;
	Ref<ArrayMesh> tile_filled_mesh;
	bool tile_meshes_dirty = true;
	
	struct PhysicsLayer {
		uint32_t collision_layer = 1;
		uint32_t collision_mask = 1;
		Ref<PhysicsMaterial> physics_material;