The calcification thing happened to me last year. Very odd, but do yours look very windowed? Can you pretty much see inside them without even candling? That's how mine were.

If you are worried about how wet or dry your eggs are, try the substrateless method. Probably a google search of the forum can explain it better than I can.

https://www.google.com/search?q=ball...w=1680&bih=920

What do you mean "bad on one side"?

As far as what to do now, Probably just wipe any mold off as needed but generally try to leave them alone. I know its hard. I lost all but one egg last year when this happened. Nothing I could do. Not to say it will happen the same way with you, but it's just how things go sometimes.