### 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)
}
				} else {
					p_dir->files[idx]->verified = true;
				}
			}
		}
		da->list_dir_end();
	}
	for (int i = 0; i < p_dir->files.size(); i++) {
		if (updated_dir && !p_dir->files[i]->verified) {
			
			ItemAction ia;
			ia.action = ItemAction::ACTION_FILE_REMOVE;
			ia.dir = p_dir;
			ia.file = p_dir->files[i]->file;
			scan_actions.push_back(ia);
			continue;
		}
		String path = cd.path_join(p_dir->files[i]->file);
		if (import_extensions.has(p_dir->files[i]->file.get_extension().to_lower())) {
			
			uint64_t mt = FileAccess::get_modified_time(path);
			bool reimport = false;
			if (mt != p_dir->files[i]->modified_time) {
				reimport = true; 
			} else if (!FileAccess::exists(path + ".import")) {
				reimport = true; 
			} else {
				uint64_t import_mt = FileAccess::get_modified_time(path + ".import");
				if (import_mt != p_dir->files[i]->import_modified_time) {