### 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 (p_to_pos >= 0 && p_to_pos <= terrain_set) {
		terrain_set += 1;
	}
}
void TileData::move_terrain_set(int p_from_index, int p_to_pos) {
	if (p_from_index == terrain_set) {
		terrain_set = (p_from_index < p_to_pos) ? p_to_pos - 1 : p_to_pos;
	} else {
		if (p_from_index < terrain_set) {
			terrain_set -= 1;
		}
		if (p_to_pos <= terrain_set) {
			terrain_set += 1;
		}
	}
}
void TileData::remove_terrain_set(int p_index) {
	if (p_index == terrain_set) {
		terrain_set = -1;
		for (int i = 0; i < 16; i++) {
			terrain_peering_bits[i] = -1;
		}
	} else if (terrain_set > p_index) {
		terrain_set -= 1;
	}
}
void TileData::add_terrain(int p_terrain_set, int p_to_pos) {