### 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)
fi->uid = ResourceLoader::get_resource_uid(path);
				}
			} else {
				fi->type = ResourceFormatImporter::get_singleton()->get_resource_type(path);
				fi->uid = ResourceFormatImporter::get_singleton()->get_resource_uid(path);
				fi->import_group_file = ResourceFormatImporter::get_singleton()->get_import_group_file(path);
				fi->script_class_name = _get_global_script_class(fi->type, path, &fi->script_class_extends, &fi->script_class_icon_path);
				fi->modified_time = 0;
				fi->import_modified_time = 0;
				fi->import_valid = fi->type == "TextFile" ? true : ResourceLoader::is_import_valid(path);
				ItemAction ia;
				ia.action = ItemAction::ACTION_FILE_TEST_REIMPORT;
				ia.dir = p_dir;
				ia.file = E->get();
				scan_actions.push_back(ia);
			}
		} else {
			if (fc && fc->modification_time == mt) {
				
				fi->type = fc->type;
				fi->resource_script_class = fc->resource_script_class;
				fi->uid = fc->uid;
				fi->modified_time = fc->modification_time;
				fi->deps = fc->deps;
				fi->import_modified_time = 0;
				fi->import_valid = true;
				fi->script_class_name = fc->script_class_name;
				fi->script_class_extends = fc->script_class_extends;
				fi->script_class_icon_path = fc->script_class_icon_path;