This isn’t a bug, but rather expected behavior. Save states are not always compatible with newer Citra builds, nor is it recommended to rely solely on them for recording your progress, as they are a lot more unstable than in-game save files. Their recommended usage is within single gaming sessions, not beyond them.
Regardless, if you have important progress saved only on a save state that you can’t load anymore, upload a log file and tell me what save state slot you’re trying to load. I should be able to find the Citra build that can load your save state, after which you can save in-game to continue playing on the latest Citra builds.