You need to activate External Save Directory before upgrading.
Viewing post in Lost all progress after updating
I know it's very late and probably doesn't matter anymore, but in my case I did make sure it was activated and lost my saves anyway. It may have been due to some display glitch but who knows.
It was depressing since I was so far in and the game is so good and challenging. Only now months later I'm starting a new playthrough. RIP Slime Jr.