Need help with incubator!

Normally/ideally they are left in for the first few days because eggs benefit from an environment higher in carbon dioxide initially, which the eggs transpire throughout incubation. I think that is why they are designed that way.
In fact, they could be left in till day 10. There are already minute holes in both top and bottom of those incubators for ventilation before the plugs are removed.
(I used to leave both in till day 4 or 5 and pull the second one by day 10),
The reason for this is that when an egg is laid, the albumen contains a significant amount of CO2. since it is a much higher concentration than that in ambient air, a great deal diffuses or transpires out of the egg.
While oxygen is necessary for life, during incubation, monitoring CO2 concentration is more important. During the first 10 days of incubation, the oxygen demand from the embryo is very low because of low metabolism. Keeping the plugs in will also keep temperature and humidity more stable.
By removing the plugs on different days allows a bit of fine tuning of CO2 and O2. When the incubator is sealed the firs few days, it not only raises CO2 but also humidity so weight loss during that time may have to be compensated for later. For that reason, I think it is important to monitor weight loss throughout incubation.
 
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Relax, you are not in any trouble. A lot of what we know about incubation was developed in studies paid for by the commercial operations, They regularly use incubators that might hold 60,000 eggs at a time. They pay for the studies so they study their conditions, not ours. We can gain a lot of insight from their studies but some of that may not apply to us as much as it does them.

Yes, as Canoe said, early in incubation the developing embryo does not need a lot of fresh oxygen, they may do marginally better in a higher carbon dioxide atmosphere. But the more the embryo ages the more benefit they get from fresh air. I don't have a specific day that they make that switch, I doubt if their is one. I suspect it is a gradual change. I personally would not wait that long to pull the plug, ten days sounds about right, but that is just a guess.

The egg shell is porous and air passes through it. The carbon dioxide level is going to be higher inside the shell than outside it. I would not want the air cell to have a really high concentration of carbon dioxide when the chick internal pips and starts breathing that air instead of living in a liquid environment. It is breathing before it external pips.

When you remove one or both of those plugs the humidity inside will drop. It should hold temperature OK. I don't know how that incubator handles humidity, I adjust mine by which water reservoirs I fill. Even if it weren't for the fresh air issue I'd want the plug out and humidity stabilized when I went into lockdown.

My incubator only has one ventilation plug, I never close it. If you are using an incubator with 60,000 eggs just a small percentage change in hatchability can mean a lot of chicks over the course of a year. With mine and as seldom as I use it I doubt I'd notice a difference by playing with the plug. I think temperature, humidity, and turning are much more important. I do understand the desire to improve the incubation conditions as much as you can. Absolutely nothing wrong with leaving those plugs in early in incubation. I just don't think I'd notice a difference.

Good luck.
 

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