Kiddos eat Sharpies all the time and they don't die. I mark my eggs with Sharpie and have yet to hatch a two headed chick.
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This argument was put to rest several years ago. Sharpie is ok.
Have you candled the eggs again? I have one that has a dark shell that I'm unsure of and am waiting till day 10 on.. A link on the incubation 101page has pictures of early embryotic death that make a ring.. Please keep us posted!