### 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)
reimport = true;
				} else if (_test_for_reimport(path, true)) {
					reimport = true;
				}
			}
			if (reimport) {
				ItemAction ia;
				ia.action = ItemAction::ACTION_FILE_TEST_REIMPORT;
				ia.dir = p_dir;
				ia.file = p_dir->files[i]->file;
				scan_actions.push_back(ia);
			}
		} else if (ResourceCache::has(path)) { 
			uint64_t mt = FileAccess::get_modified_time(path);
			if (mt != p_dir->files[i]->modified_time) {
				p_dir->files[i]->modified_time = mt; 
				ItemAction ia;
				ia.action = ItemAction::ACTION_FILE_RELOAD;
				ia.dir = p_dir;
				ia.file = p_dir->files[i]->file;
				scan_actions.push_back(ia);
			}
		}
	}
	for (int i = 0; i < p_dir->subdirs.size(); i++) {
		if ((updated_dir && !p_dir->subdirs[i]->verified) || _should_skip_directory(p_dir->subdirs[i]->get_path())) {
			
			ItemAction ia;
			ia.action = ItemAction::ACTION_DIR_REMOVE;
			ia.dir = p_dir->subdirs[i];