Hello! Thank you for playing!
That sounds like an itch.io client issue to me. I haven't used it, so I don't know how it works, but maybe there's a refresh button somewhere? Or maybe it needs to be restarted to "forget" the old version.
About the save file corruption warning, it's mainly for versions 3 and earlier. Version 4 and 5 have some additional mechanisms to prevent corruption so it shouldn't happen.