It shouldn't - which platform are you playing on? (Windows, MacOS, Linux, Android, SteamDeck?) We'll add in some extra testing to make sure that existing saves are preserved. The only time I can see this happening is if you're on Android and you uninstall the game before installing the latest. If you remove the game then yes - all save files will be removed with it. If you download the latest APK it should just update the existing one while preserving your saves.