Okay, so it looks like this isn't an arturia mystery. It looks like the other piece of hardware I have that has memory, the Prophet Rev 2, also has lost all of the saved banks, although in this case the user patch banks are just reset back to the factory.
Not sure what the common connection here is... I'm speculating but it seems unlikely there would be an electrical issue that would impact both in a similar way so it seems more likely that something from the PC (cakewalk?) or possible the SL MK3 (unlikely?) sent some kind of erase or reset command.
