Should I separate bad eggs?

[Bogertophis]

Truth be told, whatever mold is on the bad ones is going to spread to the good ones even more if you really get in there and disrupt them. Next clutch if you separate right away, if one goes back you can pull it quick and won't have that issue. If you are set on trying to separate them, I'd wrap the bad ones with a damp paper towel to sort of shield most of the mold from getting stirred up while you are working on them, and work on them outside the tub so mold doesn't get all over the substrate.

That's a real good idea, to wrap the moldy one with a damp paper towel if you try to separate them, etc.