### 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 (cf->has_section("remap")) {
				if (p_custom_importer.is_empty()) {
					importer_name = cf->get_value("remap", "importer");
				}
				if (cf->has_section_key("remap", "uid")) {
					String uidt = cf->get_value("remap", "uid");
					uid = ResourceUID::get_singleton()->text_to_id(uidt);
				}
				if (!p_generator_parameters) {
					if (cf->has_section_key("remap", "generator_parameters")) {
						generator_parameters = cf->get_value("remap", "generator_parameters");
					}
				}
			}
		}
	}
	if (importer_name == "keep") {
		
		fs->files[cpos]->modified_time = FileAccess::get_modified_time(p_file);
		fs->files[cpos]->import_modified_time = FileAccess::get_modified_time(p_file + ".import");
		fs->files[cpos]->deps.clear();
		fs->files[cpos]->type = "";
		fs->files[cpos]->import_valid = false;
		EditorResourcePreview::get_singleton()->check_for_invalidation(p_file);
		return OK;
	}
	Ref<ResourceImporter> importer;
	bool load_default = false;