It looks like the unraid vikunja app does not use a separate database, only the default SQLite. It also looks like the unraid app does not persist the SQLite db file. That means it is only stored inside the container and everything is lost when restarting (or upgrading it, for that matter) the container. In that case the only way to get your data back is to restore from backup (because you created a backup, did you?).
Further the app should be updated so that this does not happen in the future.
Discussion in the Vikunja forum about this: https://community.vikunja.io/t/after-updating-to-0-20-0-no-login-user-does-not-exist/937/6