### 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)
uint64_t current_mtime = FileAccess::get_modified_time(p_dir->get_path());
	bool updated_dir = false;
	String cd = p_dir->get_path();
	if (current_mtime != p_dir->modified_time || using_fat32_or_exfat) {
		updated_dir = true;
		p_dir->modified_time = current_mtime;
		
		
		for (int i = 0; i < p_dir->files.size(); i++) {
			p_dir->files[i]->verified = false;
		}
		for (int i = 0; i < p_dir->subdirs.size(); i++) {
			p_dir->get_subdir(i)->verified = false;
		}
		
		Ref<DirAccess> da = DirAccess::create(DirAccess::ACCESS_RESOURCES);
		Error ret = da->change_dir(cd);
		ERR_FAIL_COND_MSG(ret != OK, "Cannot change to '" + cd + "' folder.");
		da->list_dir_begin();
		while (true) {
			String f = da->get_next();
			if (f.is_empty()) {
				break;
			}
			if (da->current_is_hidden()) {
				continue;
			}