Mike,
I believe that I know why your eggs died.
Firstly, like I mentioned before, condensation inside the egg containers is normal in the last one-third of the incubation period. It is actually a good sign, a sign that the eggs are alive. If I don't see the condensation, then I worry.
Secondly, your egg-containers were plenty well ventilated. The closure on a sweater box is so non-tight that no extra ventilation holes are necessary, at any stage of incubation. You were probably getting ten complete air exchanges per day. The extra vent holes you drilled were superfluous. Unless the sweater box was enclosed in another airtight container like a cooler or ice chest with a tight seal, the eggs were getting more than enough air.
It is almost impossible to provide enough air circulation to prevent condensation in the last third of the incubation period. The only important issue here is to make sure that water drops don't fall onto the eggs. It may be necessary to dry the underside of the lid from time to time to prevent this.
What killed your eggs was too dry of a substrate, not too wet. Again, like I mentioned in another post, Indigo eggs must be in contact with a moist substrate in the second half of the incubation period. Since they are warmer than the air around them during this time, they can't absorb enough water from the humid air and end up losing water. In the first half of the incubation, Indigo eggs will be fine on a foam substrate in moist air. They can absorb water from the air. In the second half of the incubation, they become too warm to do this, and they must then be in contact with a moist substrate.
From the added information you just mentioned, your eggs had the classical symptoms of dehydrated eggs. The condensation in the container indicated that they were alive. They were collapsing due to loss of water. Dehydrating eggs frequently collapse from underneath and go unnoticed as a result. Indigo eggs can tolerate a small degree of dehydration/collapse and still hatch. Too much and they will die.
Perlite is a poor choice for incubation substrate in my opinion. Even if it is moist, eggs don't make enough physical contact with it to be able to absorb water. Vermiculite is a much better choice. Its soft nature allows a better contact area with eggs. Eggs can absorb water readily from it.
I would speculate that the perlite you used became more dry around the outsides of the container. The egg in the middle survived because it was able to get a little more water from the moister perlite in the center. I would also suspect that this egg collapsed too, due to dehydration, just not as much as the others. Tell me if I am right.
I will try to post a fail-safe method for Indigo egg incubation soon. Remind me if I forget. Next year will be better.
Robert Bruce
robert.bruce@sbcglobal.net (310) 502-6311