There is nothing wrong with removing eggs - there is just more things that can go wrong with an incubator than if mom sits on them - you could have temp problems, you can have humidity problems, air circulation problems, accidents, etc. etc. these are all things that the mother would naturally compensate for.
As for this big issue about it being stressfull on the mom - studies show other wise - Aubret, F., Bonnet, X., Shine, R. and Maumelat, S. 2005. Energy expenditure for parental care may be trivial for brooding pythons, Python regius - interesting reading. On top of that my female was off feed for a total of 5 months (my females I'm breeding now are still feeding) - no different than any other snake that goes off feed for the winter - her total weight loss was around 20 grams.
There is also another study that shows that maternally incubated hatchlings hatch bigger and stronger than artifically incubated eggs - due to less desiccation and higher yolk consumption by the embryo. Gotta see if I can find that article - vaguely recall the details.
I am certainly not an advocate for maternal incubation or anti-incubator - nor do I really think one is "better" than the other - I think for the most part it's a control issue for most people.
But I've been known to be wrong before tho.
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Tosha 
"Nihil facimus sed id bene facimus"

10.35.0 Ball Python (Harry and Fluffy and gang)
1.0.0 Angolan Python (Anakin Skywalker)
0.0.1 Green Tree Python (Verdi - yeah I know but my kids love the book)
0.1.0 Bredls Python (Smurfette)
0.2.0 Feline (Pippen and Pandora)
0.0.1 Desert Tortoise (Pope John Paul aka JP )
2.2.1 Fish (1,2,3,4)
0.0.1 Lizard rescued from feline
0.0.0 frogs rescued from pool skimmer