Depending on the number of locos you have, it is probably best to standardize on the new Scale Speed motors going forward. All new Atlas locos have the Scale Speed motor, and at some point Atlas will most likely discontinue older parts.
Plus the Scale Speed motors gives much better performance at low-speeds.
The latest Scale Speed motor for the GP9 is Atlas Part 480100 (light gray plastic).
The Atlas Parts website remains offline for upgrades, but I called them on the phone and they were super-helpful and shipped my order quickly.
Cheers