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It's not common but not impossible that he has weak digestive enzymes for whatever reason. I had a rattlesnake many years ago that was like that, but his situation was made worse (& thereby obvious) by whoever made him "venomoid". He was given to me, able to eat but unable to digest fats, resulting in greasy foul-smelling stools; his body was thin (triangular). Venom starts the digestive process, & while perhaps most snakes have good enough digestion that they don't "miss" using venom, obviously it was a huge problem for him. (I used a venom donor to envenomate rodents for him.)
Obviously since I wasn't the original owner of that snake I can't tell you if he was born that way (weak digestion) but I'm assuming he was. He was an adult snake when he came to me, & from that experience, I have to assume that some small percentage of snakes might suffer likewise, cause unknown.
You say this snake has been like this for 3 years? A snake that is slowly starving is probably NOT producing digestive enzymes: they need to eat enough to keep up with all their bodily functions & I believe that if he got more nutrition, he might slowly regain his digestive abilities, if what you say is true (no physical blockages). I don't blame you for not wanting to euthanize him, but you need to do more for him than what you've been doing, IMO. It may take a while, not just one tube-feed: I've always used Gerber's (2nd foods) chicken babyfood, thinned w/ water. Do not try to feed a large amount at once: even though it's easier to digest, you want to gradually increase the amount...see how he does & let us know?
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