I have never had, thank God, a need to have a lens realigned. I do not know the expense involved. I believe that alignment is very important in an enlarging lens. It therefore follows that I would be very concerned that the alignment be done properly. Unless I was given a recommendation by some one who had has a good deal of experience in having lenses realiged and in whom I had much reason to trust their judgement I would return it to the distributor..Schneider or Rodenstock.. for realignment making certain I was first given a quote.
Frankly, given the number of people that are leaving darkroom practice very fine used enlarging lenses are inexpensively available. If, for instance, the lens I was interested in getting as a replacement was a 90mm Apo-Rodagon, I would view Ebay sales history to see what they have been bringing for mint- examples so that I could make an informed decision.
Good luck.