@TeddyKrajeski You were playing games in franchise without the issue and then it happened mid season? From what we heard thus far, it would only happen in Franchise if you created your franchise after the issue had already flipped your lines changes to none and then you started a franchise with those base settings. Would be good to know if you have a difference experience.
Or did you sim a lot of games and then only notice the issue later on? Just wondering how you got through 2 seasons without seeing it.
Also, as a workaround for having your season already started, are you able to change your line change settings from within franchise as you go into a game by going to the game settings and switching the line changes from Off to Auto for the team you are controlling? Since it seems you are simming, you could do that once for when your team is home and once when they are away (since the opposition team will be greyed out and unable to be changed) and it should save from them on.
If you change it before going in to play the game and back out and sim those games until you get one home and one away, it should still save by switching it and backing out to sim the game.