Hi sethsleader! My incubator always gets a bit "wiffy" a day or two into the hatch--all those fluids in that warm, humid environment, makes for some interesting "aromas."
I know it's sacrilege, but I only leave babies in the incubator for 24 hours (ish). That's actually the recommendation from Dave Holderread (Storey's Guide to Raising Ducks), and I do it mostly because by 24 hours old, the ducklings are usually playing with the fan (getting their bills scratched up), poking at the heat element, pooping on the remaining eggs, knocking over the equipment, and generally causing all kind of ruckus in there.
So at 24 hours, I take out all the ducks that are hatched and fluffed (if one is fluffing, I'll leave them a little longer till it's close to done).
Then I leave it alone another 24 hours, and repeat until the hatch is done.
Now, the disclaimer: I've only done two batches of eggs, hatching out a total of 12 eggs at a hatchability rate of around 65%. This is not a stellar hatch rate. However, on this last batch the four eggs that did not hatch all seem to have died before hatch day, and I did not lose even one egg that pipped--all pippers eventually hatched. So, I don't think the humidity at the end was a problem. But obviously, after only two hatches, I'm no expert.
On the other hand, Holderread certainly *is* an expert, and here is what he does (page 155, Storey's Guide): "On Monday and Tuesday mornings, the hatcher is opened, the trays removed, and the ducklings taken out. The unhatched eggs are returned to the hatcher and lightly sprayed with lukewarm tap water to soften the shell membranes, which may have dried out while out of the machine. On Wednesday morning, the remainder of the hatch is taken off."
He claims hatch rates of 75-95% of fertilized waterfowl eggs (he doesn't do chickens).
