You should have tossed the eggs. Toss them immediately, If you remove the built-up crap, the parents will desert that nest. As for the youngsters, the older they are the safer you are. If they're less than say, 15 days old, you can clean the loft floor but should probably leave the youngsters where they are, in a circle of hard crap, or the parents may desert them. If you remove all the crap and install hay around the youngsters, the parents may refuse to look after them. Wait until the youngsters reach 21 days and you can do whatever you want to clean the floor and nest--the youngsters will survive just fine and the parents will look after them until they're weaned, which can occur any time after 21 days, but you may want to wait longer, and remove them from the parents as soon as they start flying up to the perches and show that they know how to eat and find the water on their own.