We are looking into the cause of this issue and hopefully we can find a solution. Unfortunately we have been unable to reproduce this issue locally, so we do not have an official workaround. However, another user who did experience this issue claimed to fix it by copying their save from slot 1 to slot 3 and then playing in slot 1 by starting the last episode where they had save data. To simplify this with an example, if you had a save from episode 4, and loading that save started episode 1, copy your save from slot 1 to slot 3, then load episode 4 in slot 1. The desired result is episode 4 will start at the point you last left off. We cannot confirm this works, but if your save now says episode 1, it's worth a shot to try to regain your progress in the last episode you played.
If anyone affected prefers to wait, I will send out updates as soon as I know anything.