I'm very sorry to hear this. Removing an egg that is doing poorly is very risky to the healthy eggs though. If you're only a few days from hatch and a bad egg doesn't just come free without any pulling or cutting it is still best to just leave it be so as to not risk tearing a hole in a good egg. Good eggs are amazingly resistant to mold.
All in all you did the best you could and I doubt cutting sooner would have done anything as an underdeveloped hatchling rarely has good lungs.
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