### 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 (idx == -1) {
					
					EditorFileSystemDirectory::FileInfo *fi = memnew(EditorFileSystemDirectory::FileInfo);
					fi->file = f;
					String path = cd.path_join(fi->file);
					fi->modified_time = FileAccess::get_modified_time(path);
					fi->import_modified_time = 0;
					fi->type = ResourceLoader::get_resource_type(path);
					fi->resource_script_class = ResourceLoader::get_resource_script_class(path);
					if (fi->type == "" && textfile_extensions.has(ext)) {
						fi->type = "TextFile";
					}
					fi->script_class_name = _get_global_script_class(fi->type, path, &fi->script_class_extends, &fi->script_class_icon_path);
					fi->import_valid = fi->type == "TextFile" ? true : ResourceLoader::is_import_valid(path);
					fi->import_group_file = ResourceLoader::get_import_group_file(path);
					{
						ItemAction ia;
						ia.action = ItemAction::ACTION_FILE_ADD;
						ia.dir = p_dir;
						ia.file = f;
						ia.new_file = fi;
						scan_actions.push_back(ia);
					}
					if (import_extensions.has(ext)) {
						
						ItemAction ia;
						ia.action = ItemAction::ACTION_FILE_TEST_REIMPORT;
						ia.dir = p_dir;
						ia.file = f;
						scan_actions.push_back(ia);