Just my two cents.. If its day 56, unless it's been exactly 89 degrees in your room and/or the snakes cage the entire time the eggs have been in there, and the humidity has been very high, those eggs may never hatch.. They roam around your room and the temps are falling?
People who use an incubator end up with dead and deformed babies with even the slightest temperature fluctuations and/or humidity lower than 90% which allows the eggs to begin collapsing earlier than a week or two prior to hatching.
Maternal incubation can be difficult unless you're providing a very controlled environment which it doesn't sound like you have. I'm interested in seeing in update when the eggs hatch if they do. If they do, don't be surprised if they don't hatch until much later than 60 days. At lower temperatures they develop much slower.
As for leaving the male in there. The cons to doing so are causing the female stress which in turn may cause her to leave the eggs when she shouldn't. Or if they hatch, he could crush the babies with his size. As could momma.
There are also few cases of snake cannibalism. It's rare but possible.
Ball pythons are solitary animals. If you want to talk about "natural" then there you go.. They are solitary in nature.
By the way.. My snakes are my pets also. Even the ones I breed. Try to harm my 10 year old girl that I've raised from her first meal and I'll show you what my pet means to me even though shes given me a few clutches..
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