### 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)
f->store_line("importer_version=" + itos(version));
			}
			if (!importer->get_resource_type().is_empty()) {
				f->store_line("type=\"" + importer->get_resource_type() + "\"");
			}
			if (uid == ResourceUID::INVALID_ID) {
				uid = ResourceUID::get_singleton()->create_id();
			}
			f->store_line("uid=\"" + ResourceUID::get_singleton()->id_to_text(uid) + "\""); 
			if (err == OK) {
				String path = base_path + "." + importer->get_save_extension();
				f->store_line("path=\"" + path + "\"");
				dest_paths.push_back(path);
			}
			f->store_line("group_file=" + Variant(p_group_file).get_construct_string());
			if (err == OK) {
				f->store_line("valid=true");
			} else {
				f->store_line("valid=false");
			}
			f->store_line("[deps]\n");
			f->store_line("");
			f->store_line("source_file=" + Variant(file).get_construct_string());
			if (dest_paths.size()) {
				Array dp;
				for (int i = 0; i < dest_paths.size(); i++) {
					dp.push_back(dest_paths[i]);
				}
				f->store_line("dest_files=" + Variant(dp).get_construct_string() + "\n");
			}