Technogrim's post in HD500X Times Out While in Edit? was marked as the answer
I have determined that it was indeed the usb ports.
It seems certain ports cut out occasionally and some don't work at all.
But I managed to find one and was able to edit and add a bunch of pedals to an entire brand new preset and saved it with no issues.
I'm super relieved....I guess it's time for a new motherboard.