Again speaking anecdotally, I left them in there. After all had pipped, I cleaned out the same tub, lined it in wet paper towels, and set the eggs on that. When they all emerged I removed the shells, replaced the paper towels with clean wet ones, and left them in there until they shed.
Actually, I don't have the rack I was supposed to have for when these guys arrived, so they are STILL in the incubator in their own little 6 qt containers with a light on (just to give them daylength) and they are eating and growing quite happily 
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26 year old 0.1 from Lincoln, NE
Ball Pythons - 0.1 Silver Bullet, 0.1 Pastel, 1.0 Pastel het Pied, 0.1 Pied, 0.1 Cinn, 1.0 Black Pewter, 1.0 Woma, 0.1 Yellowbelly, 2.1 Normals
Kingsnakes - 1.0 L. m. thayeri, 0.1 L. m. thayeri X L. alterna, 1.0 L. g. californiae
Other - 0.1 Whitesided P. catenifer sayi, 1.0 H. nascicus, ?.? Chrysemys picta, 1.0 husband, ?.? Mini-human