Well I dont know if ever an Amtrak train went over MILW tracks between Harlowton and Avery - where the Joes once served.
But I remember about some information I once collected from the internet that during a time Amtrak trains has been rerouted from NP tracks via MILW tracks between Easton, Wa (west of Ellensburg) and Auburn, Wa (near by Tacoma).