Hello again Jonathan!
You may find some useful information from a similar post here: AutoTune doesn't restart after centering vehicle
I’m afraid I’ll be travelling shortly and won’t have time to go in depth, but I wish you luck in getting the AutoTune completed! Just remember that it may not resume unless the throttle is exactly where it was when you initiated the AutoTune, or at exact mid-throttle. It can be finicky!
Cheers,
Adam