oh, infection is incredibly taxing on the system! No wonder his eggs didn't do well. I wouldn't worry about it, wait til he's well 100%. Also, antibiotics can affect sperm.
I use something sharp and strong to poke a small hole in the top (air cell end so you don't poke/scratch the baby) then you can chip off small, very small pieces to see what's going on in there.
The first kind of eggs are bad, the second set of eggs are probably shrink wrapped or dead in shell. I would open a small window in the top of the egg to see if there is any movement. They are past due date right?