I believe you are supposed to remove the good eggs from the infertile eggs in the beginning for this same reason. In the most recent snake bytes episode, Bryan talks about it because by leaving the infertile eggs you risk the infertile ones rotting and hurting the good ones. I would believe that you could still remove them now without hurting the eggs as long as you don't spin the embryo around, however hopefully someone else can chime in to be 100% sure
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