I would probably just go through the new matchups and force every outcome as the commish to make everyone’s records what they were prior to this happening, and then just keep the new schedule going forward. Weird bug, but if you’re positive it wasn’t done purposely, there is not much else you can do because I would think thag not everyone remembers every matchup.
Whether it is skill or luck, does not matter. We all play it to have fun. Recognizing that there is at least an aspect of luck is part of not allowing this game to consume you too much. I have been playing for 10+ years and after recently (3 years ago) realizing I can’t control too much other than my lineup decisions and who I draft/waivers, you enjoy it a lot more.