### 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)
if (!importer_name.is_empty()) {
		importer = ResourceFormatImporter::get_singleton()->get_importer_by_name(importer_name);
	}
	if (importer.is_null()) {
		
		importer = ResourceFormatImporter::get_singleton()->get_importer_by_extension(p_file.get_extension());
		load_default = true;
		if (importer.is_null()) {
			ERR_FAIL_V_MSG(ERR_FILE_CANT_OPEN, "BUG: File queued for import, but can't be imported, importer for type '" + importer_name + "' not found.");
		}
	}
	if (FileAccess::exists(p_file + ".import")) {
		
		importer->handle_compatibility_options(params);
	}
	
	List<ResourceImporter::ImportOption> opts;
	importer->get_import_options(p_file, &opts);
	for (const ResourceImporter::ImportOption &E : opts) {
		if (!params.has(E.option.name)) { 
			params[E.option.name] = E.default_value;
		}
	}
	if (load_default && ProjectSettings::get_singleton()->has_setting("importer_defaults/" + importer->get_importer_name())) {
		
		Dictionary d = GLOBAL_GET("importer_defaults/" + importer->get_importer_name());
		List<Variant> v;
		d.get_key_list(&v);
		for (const Variant &E : v) {