### 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)
fs->files[cpos]->modified_time = FileAccess::get_modified_time(file);
		fs->files[cpos]->import_modified_time = FileAccess::get_modified_time(file + ".import");
		fs->files[cpos]->deps = _get_dependencies(file);
		fs->files[cpos]->uid = uid;
		fs->files[cpos]->type = importer->get_resource_type();
		if (fs->files[cpos]->type == "" && textfile_extensions.has(file.get_extension())) {
			fs->files[cpos]->type = "TextFile";
		}
		fs->files[cpos]->import_valid = err == OK;
		if (ResourceUID::get_singleton()->has_id(uid)) {
			ResourceUID::get_singleton()->set_id(uid, file);
		} else {
			ResourceUID::get_singleton()->add_id(uid, file);
		}
		
		
		Ref<Resource> r = ResourceCache::get_ref(file);
		if (r.is_valid()) {
			if (!r->get_import_path().is_empty()) {
				String dst_path = ResourceFormatImporter::get_singleton()->get_internal_resource_path(file);
				r->set_import_path(dst_path);
				r->set_import_last_modified_time(0);
			}
		}
		EditorResourcePreview::get_singleton()->check_for_invalidation(file);
	}
	return err;
}
Error EditorFileSystem::_reimport_file(const String &p_file, const HashMap<StringName, Variant> &p_custom_options, const String &p_custom_importer, Variant *p_generator_parameters) {