I don't change the substrate AT ALL. That's odd, you shouldn't have to do that.
I did wind up having to cling-wrap the tubs to keep the humidity up. I didn't have to do that last year---I think it's the new incubator with the fan blowing dry Arizona air around.
I also check on the eggs once a day, particularly as the hatch date gets closer. (Partly because I was worried about oxygen. But mostly I'm bored and I want them to hatch already.) I don't think checking on them hurts them, just your/my sanity.
There's plenty of condensation on my tubs, particularly on the side by the fridge door. Condensation means there's a temperature gradient in the incubator, so the inside of the tub is warmer than the outside. It's nearly impossible to avoid in a small incubator.
I keep the eggs away from the side of the tub, and I use a bit of the plastic light grating to keep the eggs from sitting directly in the vermiculite:
... I would definitely recommend the grating next year. Given what happened this season, you might even want to try the substrate-less incubation, with just some water in the bottom of the tub and three pieces of grating stacked to keep the eggs out of the water. I don't really like water incubation, because I do check on the eggs so frequently, and the water sloshes when I pull the tubs out.... but definitely do consider the grating on top of a slightly drier substrate next year.
And last, temperatures. A heat spike can kill a whole clutch like that. What's your incubator?
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