Two things could be occurring. One, is there a chance any predators or pests can access the eggs, i.e., rats, ants, turtles, raccoons? If something can reach into the nest or carry the eggs out (rats), then this may be the reason that the eggs are disappearing.

Two, if there is no access to the eggs except the birds, then the eggs are being buried further into the nest away from the operating section of the nest or the eggs are being rolled into the water. The birds know when something is wrong with the eggs. Even the eggs that have not been addled may be infertile, rotten or have some other problem. Swans know and will get rid of anything that does not seem right. If you are messing with the nest too much, they will abandon the eggs and the nest. The Regal Swan