I also do not fully understand however to me, it is more unlikely to be from a seperate clutch. This would mean that the female would have ovulated twice.
I have seen, this year, two baby milk snakes not rot away after six weeks while sitting in the incubator. I had cut these eggs as they were the last to pip of their clutch and since they never finished slitting the egg I helped. Both babies were unresponsive in the egg so I cut further and pulled the heads out of the egg, both were dead. I set them back in the incubator with the lid on the container and then forgot about them being in there. When I did find them again the babies had not rotted away and had only dried out a little, still looked pretty fresh actually. Not that they would have looked like this after three months.
It would just be more likely to ME that the babies had not developed as quickly as the others. I have also seen corn snakes regularly pass unlaid eggs months after laying their second clutchs.
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Steve Perry
North Idaho.

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