It is done all the time, I had it done and nothing happens other than possible shock loss.
If you mean that when they punch in the new grafts, one of those might transect an existing graft, then yes it would be killed off. However for a person with hairloss the benefits would outweigh the slight loss of a few grafts this way. So would you rather keep it how it is today or get 2500 new grafts while maybe killing off 25.