### 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)
ERR_FAIL_INDEX(p_layer_id, physics.size());
	physics.write[p_layer_id].angular_velocity = p_velocity;
	emit_signal(SNAME("changed"));
}
real_t TileData::get_constant_angular_velocity(int p_layer_id) const {
	ERR_FAIL_INDEX_V(p_layer_id, physics.size(), 0.0);
	return physics[p_layer_id].angular_velocity;
}
void TileData::set_collision_polygons_count(int p_layer_id, int p_polygons_count) {
	ERR_FAIL_INDEX(p_layer_id, physics.size());
	ERR_FAIL_COND(p_polygons_count < 0);
	if (p_polygons_count == physics.write[p_layer_id].polygons.size()) {
		return;
	}
	physics.write[p_layer_id].polygons.resize(p_polygons_count);
	notify_property_list_changed();
	emit_signal(SNAME("changed"));
}
int TileData::get_collision_polygons_count(int p_layer_id) const {
	ERR_FAIL_INDEX_V(p_layer_id, physics.size(), 0);
	return physics[p_layer_id].polygons.size();
}
void TileData::add_collision_polygon(int p_layer_id) {
	ERR_FAIL_INDEX(p_layer_id, physics.size());
	physics.write[p_layer_id].polygons.push_back(PhysicsLayerTileData::PolygonShapeTileData());
	emit_signal(SNAME("changed"));
}
void TileData::remove_collision_polygon(int p_layer_id, int p_polygon_index) {