### 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)
String source_file = "";
	String source_md5 = "";
	Vector<String> dest_files;
	String dest_md5 = "";
	int version = 0;
	bool found_uid = false;
	while (true) {
		assign = Variant();
		next_tag.fields.clear();
		next_tag.name = String();
		err = VariantParser::parse_tag_assign_eof(&stream, lines, error_text, next_tag, assign, value, nullptr, true);
		if (err == ERR_FILE_EOF) {
			break;
		} else if (err != OK) {
			ERR_PRINT("ResourceFormatImporter::load - '" + p_path + ".import:" + itos(lines) + "' error '" + error_text + "'.");
			return false; 
		}
		if (!assign.is_empty()) {
			if (assign.begins_with("path")) {
				to_check.push_back(value);
			} else if (assign == "files") {
				Array fa = value;
				for (int i = 0; i < fa.size(); i++) {
					to_check.push_back(fa[i]);
				}
			} else if (assign == "importer_version") {
				version = value;
			} else if (assign == "importer") {
				importer_name = value;
			} else if (assign == "uid") {