### 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 (da->current_is_dir()) {
				if (f.begins_with(".")) { 
					continue;
				}
				int idx = p_dir->find_dir_index(f);
				if (idx == -1) {
					if (_should_skip_directory(cd.path_join(f))) {
						continue;
					}
					EditorFileSystemDirectory *efd = memnew(EditorFileSystemDirectory);
					efd->parent = p_dir;
					efd->name = f;
					Ref<DirAccess> d = DirAccess::create(DirAccess::ACCESS_RESOURCES);
					d->change_dir(cd.path_join(f));
					_scan_new_dir(efd, d, p_progress.get_sub(1, 1));
					ItemAction ia;
					ia.action = ItemAction::ACTION_DIR_ADD;
					ia.dir = p_dir;
					ia.file = f;
					ia.new_dir = efd;
					scan_actions.push_back(ia);
				} else {
					p_dir->subdirs[idx]->verified = true;
				}
			} else {
				String ext = f.get_extension().to_lower();
				if (!valid_extensions.has(ext)) {
					continue; 
				}
				int idx = p_dir->find_file_index(f);