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Hello @bborth,
You pose an interesting question about mitochondria damage. I did some research on the topic at Google Scholar and information seems to be there about the aging process and mitochondria damage as well as the use of chemotherapy. You do not mention your age, type of abdominal surgery nor any history of chemotherapy so perhaps this is not an issue for you. I have had three surgeries of the upper digestive tract and I know that it takes longer each time to recover from the effects of surgery, anesthesia, etc.
You said that you had abdominal surgery then followed by an infection and then two antibiotics. As you may know, ciprofloxacin can cause some problems with tendons, muscles, etc. It is suggested that you do not exercise heavily when you are taking this med. Here is some info from Drugs.com which lists some of the side effects of this type of med https://www.drugs.com/ciprofloxacin.html. Are you still taking the ciprofloxacin?
Please know that it is always your right to get a second opinion. What do your doctors say about your current symptoms?
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I had Roux En Y surgery for bile reflux, not for weight loss. My surgeon says that although not likely, antibiotics can cause damage to the stomach in regard to wiping out all the bacteria, which in turn can get into the mitochondria. I have sore hip tendons now whereas I never had this in all my time of doing intense running/biking. But it is the energy that is the main issue with me, just can't generate what I was able to prior to taking this medication. A functional doctor I am seeing as well seems to be convinced this is the root of my problem now, but fixing the gut with a balanced level of bacterial/flora will start the process of healing. Could be some time though. Just not used to being this lethargic all the time, which can be depressing.