that certainly is odd. Here's a few things you can try (make sure you keep a safe backup of this main elsewhere.
1. Restart the game, play through it and save, then close the Citra fully, then replace the main with the old one, and try to proceed. If this fails
2. Try downloading a different version of Citra (one that is not nightly build) and repeat the first point.
no clue, but at this stage it appears to be a Citra issue, since there's nothing wrong with the save.
If you think it matters, I walked a few steps in the game, then saved again. main