### 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)
params[E] = d[E];
		}
	}
	
	String base_path = ResourceFormatImporter::get_singleton()->get_import_base_path(p_file);
	List<String> import_variants;
	List<String> gen_files;
	Variant meta;
	Error err = importer->import(p_file, base_path, params, &import_variants, &gen_files, &meta);
	ERR_FAIL_COND_V_MSG(err != OK, ERR_FILE_UNRECOGNIZED, "Error importing '" + p_file + "'.");
	
	Vector<String> dest_paths;
	{
		Ref<FileAccess> f = FileAccess::open(p_file + ".import", FileAccess::WRITE);
		ERR_FAIL_COND_V_MSG(f.is_null(), ERR_FILE_CANT_OPEN, "Cannot open file from path '" + p_file + ".import'.");
		
		f->store_line("[remap]");
		f->store_line("");
		f->store_line("importer=\"" + importer->get_importer_name() + "\"");
		int version = importer->get_format_version();
		if (version > 0) {
			f->store_line("importer_version=" + itos(version));
		}
		if (!importer->get_resource_type().is_empty()) {
			f->store_line("type=\"" + importer->get_resource_type() + "\"");
		}
		if (uid == ResourceUID::INVALID_ID) {
			uid = ResourceUID::get_singleton()->create_id();
		}
		f->store_line("uid=\"" + ResourceUID::get_singleton()->id_to_text(uid) + "\"");