### 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)
call_deferred(SNAME("emit_signal"), "filesystem_changed"); 
		return;
	}
	String type = ResourceLoader::get_resource_type(p_file);
	if (type.is_empty() && textfile_extensions.has(p_file.get_extension())) {
		type = "TextFile";
	}
	String script_class = ResourceLoader::get_resource_script_class(p_file);
	ResourceUID::ID uid = ResourceLoader::get_resource_uid(p_file);
	if (cpos == -1) {
		
		int idx = 0;
		String file_name = p_file.get_file();
		for (int i = 0; i < fs->files.size(); i++) {
			if (p_file.naturalnocasecmp_to(fs->files[i]->file) < 0) {
				break;
			}
			idx++;
		}
		EditorFileSystemDirectory::FileInfo *fi = memnew(EditorFileSystemDirectory::FileInfo);
		fi->file = file_name;
		fi->import_modified_time = 0;
		fi->import_valid = type == "TextFile" ? true : ResourceLoader::is_import_valid(p_file);
		if (idx == fs->files.size()) {
			fs->files.push_back(fi);
		} else {
			fs->files.insert(idx, fi);
		}
		cpos = idx;
	} else {