I mean ...I'm thinking it might have something to do with the save file compatibility feature they've added which they said "is in alpha, so it may have some kinks", but if having all your progress reset is the price of having save file compatibility, I'd rather not pay that price and would prefer it if they just took it away.
I'd rather have them fix save compatibility now then never have it at all.
It's better than having to redo content every update if it's just a once off issue with this one that they can track down and fix for future updates.