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!