Have you added or subtracted time that goes beyond the day time? Means if the time is 11:30pm and you add an hour its 00:30am, have you done something like that?
Yes I've tried something like that accidentally.
And the trainer gave me an error.
I thought maybe that somehow contributed to the current issue, and forced the 'days' backwards.
So I tried doing the opposite by forcing the clock forward, regardless of the error messages popping up, and it didn't fix it.
I've looked through CoSMOS solution, the table they provide is...Odd, and I couldn't utilize it. And I tried the basic CE stuff to try edit the day count, but I'm guessing the code is deeper than just a number it presents. So no luck on that neither.
I went from day 3 to day 7 with that bug too. But I literally just stayed on day 7 for 3 days so far by going back to 01:00 everytime I get sent to the ark. Not sure how detrimental this will be for my game. Good thing I didn't finish the main quests yet.
Unfortunately these are the things that happen when you keep asking for more and more options that mess with the game core functionality. You just have to deal with the consequences.