There's a good chance malachite green can kill the eggs. If a viable option though, I would manually remove them.
Just make sure flow is cut off when you're trying to do anything to avoid them from flying off and landing somewhere.
As for the actual procedure:
- cut off the flow in your tank.
- take the rock with the eggs out
- dip it in the mixed solution of tank water and malachite green. Take a turkey baster and blow between the polyps to get the eggs off and to ensure any parasites fall off.
- rinse it in tank water to get rid off any malachite green residue (I usually rinse it 2-3 times after)
- back in your tank
Usually if you see the eggs at one spot then nudibranches might be at other places too; so I would keep a close look at your other zoas.
Hope that helps!
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