### 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_index, physics_layers.size());
	physics_layers.write[p_layer_index].collision_layer = p_layer;
	emit_changed();
}
uint32_t TileSet::get_physics_layer_collision_layer(int p_layer_index) const {
	ERR_FAIL_INDEX_V(p_layer_index, physics_layers.size(), 0);
	return physics_layers[p_layer_index].collision_layer;
}
void TileSet::set_physics_layer_collision_mask(int p_layer_index, uint32_t p_mask) {
	ERR_FAIL_INDEX(p_layer_index, physics_layers.size());
	physics_layers.write[p_layer_index].collision_mask = p_mask;
	emit_changed();
}
uint32_t TileSet::get_physics_layer_collision_mask(int p_layer_index) const {
	ERR_FAIL_INDEX_V(p_layer_index, physics_layers.size(), 0);
	return physics_layers[p_layer_index].collision_mask;
}
void TileSet::set_physics_layer_physics_material(int p_layer_index, Ref<PhysicsMaterial> p_physics_material) {
	ERR_FAIL_INDEX(p_layer_index, physics_layers.size());
	physics_layers.write[p_layer_index].physics_material = p_physics_material;
}
Ref<PhysicsMaterial> TileSet::get_physics_layer_physics_material(int p_layer_index) const {
	ERR_FAIL_INDEX_V(p_layer_index, physics_layers.size(), Ref<PhysicsMaterial>());
	return physics_layers[p_layer_index].physics_material;
}
int TileSet::get_terrain_sets_count() const {