Help me Shut the Box
Python 3, 348
Saved 5 bytes thanks to Mathias Ettinger.
Saved 7 bytes thanks to DSM.
Ooof, this is a long one. I also hate that there's not a good way to do test cases.
from random import*
*l,='123456789'
q=['-']*9
r=randint
p=print
f=' to flip: '
while l!=q:
 p(*l,sep='');t=r(1,6)+r(1,6)*(l[6:]!=q[6:]);p('You rolled: %s'%t);d={int(input('Which lever'+f))for _ in' '*int(input('How many levers'+f))}
 if len(set(d))-len(d)+1-all(str(x)in l for x in d)+t-sum(d):exit('Game Over')
 for x in d:l[x-1]='-'
p('You win!')