Save states are not a replacement for in-game save files. Save state save the entirety of Citra’s emulation state, which mean that if you keep loading and saving upon save state loaded progress, Citra never gets to flush out any of the accumulated emulation bugs. Which in turn makes things very unstable. Additionally, save states tend to break with certain Citra updates. Therefore, their recommended use is only within single game sessions, not beyond them. You should use your in-game save files most of all to prevent the loss of progress.