We always incubate eggs until they get covered with mold for a few weeks, then we will cut them to see what went wrong. We haven't run into this with BPs yet as I have only done one clutch.
What we do with geckos though since the eggs are almost always seperated when laid is we simply move problem eggs to their own deli cup and continue to incubate. We have seen previously thought infertiles hatch, we have seen 50% covered in mold eggs hatch, and we have seen concave eggs hatch.
I am hopeing to learn how to seperate BP and retic eggs safely so we can continue to do the same. Moral of the story is, dont throw bad eggs out, incubate them until there is no possible chance that an animal inside could be living.