[NoOne]

quick fix, go to that team and "fill" with players... they will be 99% junk, fyi. so, shouldn't unbalance anything. should at least allow you to advance, maybe next day allows for more luck? if not in season or during important time period of course.. try other stuff first in that case.

does changing affiliation cause players to move around? if not don't worry about hte promotion demotion thing. i don't remember this being a probelm but i may have been working with empty teams, i cannot recall exactly.

somethign odd happened, either self-inflicted or a db corruption. you could export players and verify teamid's are not off for some reason, i guess.

test with backup, because it saves so much time while doing it. move a player, see of anythign shifted, if no players move around the AI has not run any process to do so... usually this requires a change of day or an even to start -- like opening day causes a 'setup entire system' to be run for AI. ( just as if you clicked it for your team in Rosters and Transactions screen)

if you save the game after re-doing the affiliations, i don't see how it could revert.

double chekc settings rules, make sure soemthign isn't causing it.. like some rule for 1:1 mlb:mil teir or something -- no, i don't think that exists, lol. but, there's so many options and settings, it's possible i'm not thinking of the potential cause off the top of my head.