Are you sure? I've reared literally thousands of butterflies and moths and even when you have a brood upwards of 250 you're lucky to have 10 pupate at once. Not saying it isn't possible but it's highly unlikely. The only other way I know of that this can happen (unless they are a dimorphic species like Phoebis philea where pupae correspond to gender, which is not the case in your sampling) is if you did it to them by temperature shocking. You can make pale monarchs this way and it changes the way the chrysalis looks as well. But obviously you would know if you let one freeze and not the others.
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