Katowoo,
Way back around 25+ years ago, when I first began raising clowns, I had just "assumed" that lifting the unhatched eggs out of the water would somehow damage them. This was partially based on the knowledge that turning a bird's egg during incubation certainly can kill them. So - I would try really hard to move the egg mass while still submerged, but they would sometimes be exposed to the air anyway - yet they would often still hatch. After reading Joyce's book, and then Matt's book, I'm a bit less worried about this now. I think more of an issue is improper agitation of the close-to-hatching eggs, or pulling them too late. If this isn't done just right, the eggs don't hatch on the proper night, and then the next night, some hatch, but most don't, and you see high mortality.
I really hate to say this - but my best success is to dip out the larva from the main tank the night they are planned to hatch out, and moving them a few at a time to the rearing tank. The real reason I dislike this is that my staff gets time and a half OT for this work - making for some REALLY expensive clownfish! (grin)
Jay