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I incubate mottled eggs, I haven't noticed any difference?

The broody hen shouldn't really be sitting on eggs longer than 25- 28 days. Her health takes a toll. I would remove the eggs that aren't up to development. You can just discard them, or put them into an incubator and keep an eye on them daily. It'd be easier to discard them, but it matters how...

By the way, day 15 eggs should be at least half full or half dark...

Seal the crack with some nail polish or liquid bandage. Just keep incubating the eggs until you can see definite growth or lack there of. Mark the eggs she's sitting on so no other hens can "add" eggs, and so you won't have staggered hatches.