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@smokesniffer There's your problem. In the four hours from the time you poked them until you cooked, the potato holes oxidized. Just like when peeling potatoes, or making fries. If you don't get them in water, they will turn black in short time (Leave a slice of raw potato on the counter for a couple hours and see what color is ends up) No reason to poke them, but if you do, do it right before cooking.
I've never gone hot to low, only the other way around. I would imagine you will need to stir and add more lump, since a 90 minute pizza cook uses more lump than a 12 hour low and slow. What size Egg and what temp for the pizza?