Sorry, "everything stops" in my original post isn't clear enough: music keeps rolling, you can queue up more commands for any characters with a full ATB gauge, you can trigger the "trying to run away" animation, you can pause and unpause, but combat will stop making any progress; none of the queued character actions will happen, ATB gauges won't fill. I haven't stared at this state for longer than maybe 5 minutes, so MAYBE it eventually resolves. My solution was to just save state way more aggressively and play around the bug and revert state if I messed up.
Sorry for the late reply. I had it set to notify me and never got an email.