### 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)
if (physics_layers[i].collision_mask == 1) {
			property_info.usage ^= PROPERTY_USAGE_STORAGE;
		}
		p_list->push_back(property_info);
		
		property_info = PropertyInfo(Variant::OBJECT, vformat("physics_layer_%d/physics_material", i), PROPERTY_HINT_RESOURCE_TYPE, "PhysicsMaterial");
		if (!physics_layers[i].physics_material.is_valid()) {
			property_info.usage ^= PROPERTY_USAGE_STORAGE;
		}
		p_list->push_back(property_info);
	}
	
	p_list->push_back(PropertyInfo(Variant::NIL, GNAME("Terrains", ""), PROPERTY_HINT_NONE, "", PROPERTY_USAGE_GROUP));
	for (int terrain_set_index = 0; terrain_set_index < terrain_sets.size(); terrain_set_index++) {
		p_list->push_back(PropertyInfo(Variant::INT, vformat("terrain_set_%d/mode", terrain_set_index), PROPERTY_HINT_ENUM, "Match Corners and Sides,Match Corners,Match Sides"));
		p_list->push_back(PropertyInfo(Variant::NIL, vformat("terrain_set_%d/terrains", terrain_set_index), PROPERTY_HINT_NONE, "", PROPERTY_USAGE_EDITOR | PROPERTY_USAGE_ARRAY, vformat("terrain_set_%d/terrain_", terrain_set_index)));
		for (int terrain_index = 0; terrain_index < terrain_sets[terrain_set_index].terrains.size(); terrain_index++) {
			p_list->push_back(PropertyInfo(Variant::STRING, vformat("terrain_set_%d/terrain_%d/name", terrain_set_index, terrain_index)));
			p_list->push_back(PropertyInfo(Variant::COLOR, vformat("terrain_set_%d/terrain_%d/color", terrain_set_index, terrain_index)));
		}
	}
	
	p_list->push_back(PropertyInfo(Variant::NIL, GNAME("Navigation", ""), PROPERTY_HINT_NONE, "", PROPERTY_USAGE_GROUP));
	for (int i = 0; i < navigation_layers.size(); i++) {
		p_list->push_back(PropertyInfo(Variant::INT, vformat("navigation_layer_%d/layers", i), PROPERTY_HINT_LAYERS_2D_NAVIGATION));
	}
	
	String argt = "Any";
	for (int i = 1; i < Variant::VARIANT_MAX; i++) {
		argt += "," + Variant::get_type_name(Variant::Type(i));