Hi. If possible, can you provide an exported save or screenshot for this error, or at least what passage you were on or what you were doing? Thanks!
I actually ran into this message a few times. I had a few characters running, which previously wasn't an issue. I tried loading up them first, which is when I instantly got the message upon clicking "Load", which may have been on me for not exporting them. But I ran into the exact same "You may continue but some parts may not work properly" in the prologue after I deleted them, closed Itch, and reopened the game. The first instance was during character customization, then during best friend customization. I wouldn't know if the full game is affected, so unfortunately I can't help you there, as I can't really get past the prologue. Hopefully this helps.