A small difference in temperature between the two boxes can make a difference in when they will hatch. In the future, you probably want to wait to cut each box individually based on one in that box pipping. Do they look fully developed? Can you tell without disturbing them if they still have a good deal left to absorb?
I've never rinsed the eggs out with water before. I'd be really worried about introducing even more bacteria and fungi. I have no idea the pH or specific gravity of the fluid in BP eggs either and how changing that could effect them. I've added small bits of sterilized water to an egg that was getting to dry, but that's different than completely replacing it.
This thread might have some helpful info how to go about raising them outside the egg if they are far enough along if the smell and color of the fluid is really concerning you. https://ball-pythons.net/forums/show...absorbing-yolk
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