Love this game, but after the update, ALL of the characters I was working on are gone. I had a level 20 or so that I just had to remake. ]: It's going to take forever for me to get back to where I was.

I had the same problem but there is a solution. Itch.io creates a new dir for the update:

You can copy your 3.3.0's save files to 3.4.8. The files can be found in this directory: ....\Itch\atlyss\ATLYSS_3.3.0a_SingleplayerDemo\ATLYSS_Data\profileCollections

I hope it works for you!