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The sad truth of classroom hatch projects is that some chicks may not survive. Teachers should prepare their students for the possibility. This way students will have an understanding of death as part of the life cycle process even if there turns out to be no problem. Further, if something does go wrong, students who are prepared for this possibility typically have an easier time dealing with the emotional aspect of a chick's passing than students who are surprised.
Occasionally, a chick will hatch out but be unhealthy, deformed, or suffering. You are the best judge of what is best for the chick and students in this situation. Euthanasia is a difficult decision, but if you are certain that the chick will die regardless and that its suffering is excessive, it can be a compassionate option. There are many ways to euthanize chicks, and the method is largely irrelevant as long as the chick's suffering is minimized by the procedure (and not extended).