I always reconcile every account daily. It no longer goes past the latest update time.
Have you tried restoring from a recent backup? We recommend saving backups frequently by navigating to File > Save a Backup... in the upper menu at the top of the screen. Provided that this has been done often, you should be able to restore from a backup that was saved just prior to when this issue emerged by navigating to File > Restore from Backup... in the same menu. I am curious about whether or not this problem continues in the restored file.