### 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 (efd->name.naturalnocasecmp_to(p_dir->subdirs[i]->name) < 0) {
						break;
					}
					idx2++;
				}
				if (idx2 == p_dir->subdirs.size()) {
					p_dir->subdirs.push_back(efd);
				} else {
					p_dir->subdirs.insert(idx2, efd);
				}
				da->change_dir("..");
			}
		} else {
			ERR_PRINT("Cannot go into subdir '" + E->get() + "'.");
		}
		p_progress.update(idx, total);
	}
	for (List<String>::Element *E = files.front(); E; E = E->next(), idx++) {
		String ext = E->get().get_extension().to_lower();
		if (!valid_extensions.has(ext)) {
			continue; 
		}
		EditorFileSystemDirectory::FileInfo *fi = memnew(EditorFileSystemDirectory::FileInfo);
		fi->file = E->get();
		String path = cd.path_join(fi->file);
		FileCache *fc = file_cache.getptr(path);
		uint64_t mt = FileAccess::get_modified_time(path);
		if (import_extensions.has(ext)) {
			
			uint64_t import_mt = 0;