then I leave them. It stinks as it goes bad but if the other eggs are healthy then they can usually "tolerate" it. I incubate all eggs even if I have a bad feeling about them from the get go. I know some cut away the bad one or "saw" it off with dental floss but I am too much of a wuss. I hate the risk of damaging the other eggs. Rotten egg juice is not pleasant or tasty. And putting eggs under running water to clean up the mess I make doesn't feel right to me..
If they are not stuck together, then pull it and incubate it in another container. If it goes bad, then discard it when you are sure it has gone bad. It is usually over when it starts to smell.
I wipe Nolvasan (diluted with water) on my funky eggs. I have had eggs develop spots/mold/fungus late in incubation but hatch fine after using Nolvasan.
Here is a picture of a egg that went bad.....with the exception of the rotten egg everything else hatched....even the one next to the rotten egg that is "seeping".

Joe Compel Reptiles