We've switched to differential updating via Itch which might explain what's gone wrong here. Unfortunately, it's to do with the Itch App and how it handles the updating of files. If you updated from a really old version, strange things might have happened.
This should work better for all updates since 0.26 as we now support the Itch App more officially, but if anybody else has this problem, uninstall the game completely and then redownload it fresh. All going well, this will only need to happen once.
You shouldn't have needed to delete your saves, they're stored in "%APPDATA%/RenPy/Sileo - Tales of a New Dawn" alongside the actual game directory itself and old save files should still be compatible with the 0.27a update.