### Godot version

v4.1.beta.custom_build [72b59325c]

### System information

Windows 10, Vulkan

### Issue description

This has been plaguing me for a while in my main project. I can only partially reproduce it in a MRP:
When placing a binary mesh resource imported from a .glb file into a MeshInstance3D, it will be gone upon restart. It doesn't seem to happen to every resource, but I've had MIs that were fine and then start doing it out of nowhere.
I thought it was going to be related to materials due to things like https://github.com/godotengine/godot/issues/77007 but I can reliably trigger it with the steps listed below.
I have done limited testing on .tres files because I usually use .res for size/performance, but in the MRP .tres doesn't seem to trigger it, so perhaps it doesn't affect those.

Note on the Steps to reproduce: you have to delete the test_cube.res and redo the steps to trigger the bug again, but in my main project the affected resources always disappear.

### Steps to reproduce

1. Double click test_cube.glb
2. Click the mesh (test_cube_Cube_097), set save to file path as: res://test_cube.res
3. Make sure to click the little folder icon and then Save (this seems to make it consistent to proc)
4. Press Reimport
5. Drag the test_cube.res to the Mesh slot of the MeshInstance3D
6. Ctrl+s to save
7. Project -> Reload current project
8. Mesh is no longer in the MeshInstance3D

### Minimal reproduction project

[binary res bug.zip](https://github.com/godotengine/godot/files/11681009/binary.res.bug.zip)
ERR_FAIL_INDEX_V(p_idx, files.size(), Vector<String>());
	Vector<String> deps;
	for (int i = 0; i < files[p_idx]->deps.size(); i++) {
		String dep = files[p_idx]->deps[i];
		int sep_idx = dep.find("::"); 
		if (sep_idx != -1) {
			dep = dep.substr(0, sep_idx);
		}
		ResourceUID::ID uid = ResourceUID::get_singleton()->text_to_id(dep);
		if (uid != ResourceUID::INVALID_ID) {
			
			if (ResourceUID::get_singleton()->has_id(uid)) {
				dep = ResourceUID::get_singleton()->get_id_path(uid);
			} else {
				continue;
			}
		}
		deps.push_back(dep);
	}
	return deps;
}
bool EditorFileSystemDirectory::get_file_import_is_valid(int p_idx) const {