Marshmallow laid an egg yesterday, and I froze it for a couple of minutes. Today, I noticed a little vein going around the egg so I froze it and gave it back. The egg was a little wet since it was melting and it absorbed the poop in the nest. I took out the egg and started picking at the poop and I accidentally cracked the egg a little, nothing spilled out, but I didn't want bacteria problems so I threw it out.

She laid another egg today so I put it in the freezer much longer than yesterday so it won't be fertile, and when I came back, the egg exploded! I completely forgot that liquid expands in the freezer, so I cracked the egg and the whole egg was frozen.

That's already 2 eggs wasted! But for her it's one since I gave her the fifth dummy egg.

How can I kill the embryo without actually killing the egg? I can try boiling it but i don't know how long...

Is she mating with a male? If so you should separate them for a while if you don't want any babies. If she continues to lay without mating just let the eggs stay until she's done sitting on them. Everytime you remove an egg she will just keep laying to replace them and thats alot of stress on her and loss of calcium and could become eggbound. If they are fertile or worried about becoming fertile remove them once laid and replace with dummy eggs.

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I can't possibly separate them. They have 3 babies right now and she is double clutching! There are 5 dummy eggs in the nest right now.

Baruch, if you want to boil them you can do it without breaking them.
I boiled mines for 4 minutes, just don't use the full flame, just a slight simmering.
Mines are still perfectly intact (no embryo of course).

Vigorously shaking the egg will also prevent it from developing.

Thank you!

I'll try boiling them. I know shaking the eggs can help but I just don't want to take chances of it still living I don't don't shake it we'll enough.

The eggs will be less likely to crack if the heat isn't too high - keep it at the 'just barely boiling' point for a few minutes, not the 'boiling like mad' point.