Incubation period needs a sustained temperature. If the temperature falls below that required for the growth inside, then it can go bad. Water as such dont have a direct impact on the eggs, many pigeons do bath while in the incubation period, but a sustained exposure to water means, its more acting as a coolant in the engine, it will take off the temperature from the eggs and cause death.
I don't think them getting a bit wet was the problem. They have a pretty good barrier around them to keep stuff like that out. It's good to keep the nesting area as dry as possible (birds still damp from bathing, don't worry about that). Wet nests lead to bacteria growth, which could then lead to sickness.
it should not be wet in the breeding area, if so you need to shore it up and have 100% dry before you let birds have babies in there. some humidity from the hen after bathing would be fine and an egg can handle some wet, but not wet as a living condition for the birds.
spirit wings is right you need to keep it dry its not good on the egges and will do serious damadge to the babies as they lose the heat real easy. if possible put a tarp over the roof till you get a chance to fix it proper.