So the eggs you thought were missing had actually been moved by the hen to another location? Sometimes that happens. You might want to check her & her nest spot for mites, maybe that's why she moved. You could change the bedding, sprinkle some insecticidal powder like 5% Sevin Dust there. Or maybe the voices in her head just told her to move. I've had eggs that seemed to be left cold too long still hatch, so let's hope that they all will continue to develop and hatch for you.