Any suggestions? BTW, its been almost a week since the battle.
Think i heard it requires a reload to before the battle and hope it doesn't happen again.
Don't know if it will work, but you could (after first saving your game just in case you mess something up) click on them in the console and try
recycleactor
According to the wikia page, that resets an NPC. I've never actually used it, though.
The cowering should end, once you talked to father. Before that, the quest doesn't register as ended and they stay in battle mode forever.