I feel for you. I had that happen under a broody chicken once, no eggs hatched.
By cleaning those eggs you remove the bloom. That is a layer on the eggs meant to keep bacteria out. It is extremely effective as long as it is intact.
If you leave that egg material on there it will attract bacteria and provide an almost certain infection that will turn the egg rotten. In my opinion they have to be cleaned.
If you clean them and put them back out in her nest I think they are certain to become infected with bacteria. I can't say it is impossible but I'd never try that.
I think your best hope for those three is to clean them, sterilize your incubator, and try to hatch them in it. Keep your hands clean when handling the eggs. Take pains to keep things clean and sanitary. Sniff the eggs as you go along and remove any that start to give the rotten egg smell.
Hatcheries clean their eggs before incubation. But they sterilize, sanitize, and have great biosecurity measures. I can't duplicate their sanitation methods at home. Those eggs may already be compromised but I think this gives you your best chances of hatching those three.
Good luck!