Just to confirm, did you put in the egg wish at the wall before going to the egg locations?
According to d2checklist, you are missing the one just outside Shuro Chi and the one between Morgeth and Vault.
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Do you have to input it every single time? Because I've done it before and gone to other eggs in separate occasions without re-entering it. I checked for the shuro one yesterday it's not there.
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To reinforce dcbaseball's comment, you need to enter the egg wish every time you go into the raid and want to see the eggs. If you exit the raid at any point, you'll need to enter it again before being able to see any eggs.
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Yes. The egg wish must be entered each time to spawn the eggs.