[Alex90]

If you leave them over night... its more than likely the parents will return and either move them to a new nest or take them into the existing burrows.

How big were the babies and were they still pinkies, begun to show pigment or had fur?

If you got you're scent on the young the female may reject them although in my experience with captive rodents (inc Guenthers voles) you can usually egt away with it once although first time mums (the rodents that is) are much more likely to reject the litter than more experienced females.

In the situation you have encountered the best thing to do provided the babies appear to be healthy and not injured or ill, is to leave them exactly where you found them without touching them or disturbing them and the female will more often than not return to more the babies within a few hours or overnight.

EDIT: Forgot to add... the chances are the babies will be gone in the morning so you should be able to put the new shed up tommorow.