This is a note from proton-ge-custom, but it may apply regardless of which Proton you use:
NOTE: Due to the symlink updates for steam cloud saves, you will want to remove your old game prefixes so that they are properly regenerated with new symlinks. Your games may not launch otherwise:
Proton Game and Prefix Launch troubleshooting:
https://www.youtube.com/watch?v=uxWJ1xvowMk
From : Release Proton-6.15-GE-1 released · GloriousEggroll/proton-ge-custom · GitHub