All settings have returned to default on my team prior to playing the last preseason game. My rules are still in place but everything else was lost.

Usually the cause of this is that you had too many plays selected in your gameplan or scouting screens, which forces the AI to reset your gameplan.

Would that have reset my misc settings as well?

This seems to come up semi-regularly... would it be possible for these re-sets to only have the "offending section" re-written, rather than the entire gameplan? E.G., if you have too many offensive plays scouted, ONLY that section would get overwritten by the AI.

I agree, that is something I need to put on the roadmap.