So there’s a mini boss in the middle of you lose your disqualified and have to start over. However the 3 extra missions after that if you lose any of those do you also get sent back to the beginning and start over or no?
You don't get sent back on the 3 extra missions. Only have to restart on the mini-bosses.
Failing a red mini boss will mean you have to restart. Failing any of the blue missions just means you don't get the extra runs added to the final boss to make it easier.