### 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)
filesystem_settings_version_for_import = l.strip_edges();
						if (filesystem_settings_version_for_import != ResourceFormatImporter::get_singleton()->get_import_settings_hash()) {
							revalidate_import_files = true;
						}
					}
					first = false;
					continue;
				}
				if (l.is_empty()) {
					continue;
				}
				if (l.begins_with("::")) {
					Vector<String> split = l.split("::");
					ERR_CONTINUE(split.size() != 3);
					String name = split[1];
					cpath = name;
				} else {
					
					Vector<String> split = l.split("::", true, 8);
					ERR_CONTINUE(split.size() < 9);
					String name = split[0];
					String file;
					file = name;
					name = cpath.path_join(name);
					FileCache fc;
					fc.type = split[1];
					if (fc.type.find("/") != -1) {
						fc.type = fc.type.get_slice("/", 0);
						fc.resource_script_class = fc.type.get_slice("/", 1);
					}