you can basically ignore the effect of your intestinal worm and whatever else by just calculating yourself the amount of calories you need to keep the same weight. Eat 2000 calories and lose 1 pound per week? your baseline is ~2500 calories. Gained a pound? your baseline is ~1500 calories.
The fact you don't absorb it all doesn't change the principle in any way. It just mean you need to recalibrate. But since you can't measure EXACTLY how many calories you're actually eating anyway or that you can predict EXACTLY how many calories you need with a calculator, you need to calibrate anyway. So really not absorbing all calories changes literally nothing about the calorie counting method.
The biggest advantage of calorie counting is it's more reliable than looking at the balance everyday because a ton of stuff will make you a few pounds heavier/lighter at any time it fluctuates too much. The scale doesn't move for weeks and people panic but really it was just random and then they lose 5 pounds on the 5th week and they think "omg, i must have lost all the weight at once because i ate that one apple!" You just can't use a scale short term. But all you have to do is count the calories, believe in the process, and if after months it doesn't work, you adjust your estimate of how many calories you burn and change your diet based on that.
I would echo this general idea of recalibrating, and add a refinement.
Instead of believing the process and waiting for months to see if it works, you can weigh yourself every day and look at the moving average. That will let you ignore the natural daily fluctuations, but still give you regular feedback.
In my experience, that regular feedback really helps with the motivation to keep doing the calorie counting.
I did that, but even then it takes weeks if not months to get a good idea from my experience. Basically, my weight would vary by 2 pounds, but i was aiming at losing 1 pound per week, so it took at least 2 weeks before my progress wouldn't get lost in the noise.
I've also heard the argument it's worse for women because weight changes with the menstrual cycles, so then you really have to look at the very least one month of data.
There's no shortage of folks who struggle to put on weight and operate under a hand-wavy explanation of "I have a high metabolism" when in fact it's likely they have a hormonal problem calorie counting is completely irrelevant in addressing.
The fact you don't absorb it all doesn't change the principle in any way. It just mean you need to recalibrate. But since you can't measure EXACTLY how many calories you're actually eating anyway or that you can predict EXACTLY how many calories you need with a calculator, you need to calibrate anyway. So really not absorbing all calories changes literally nothing about the calorie counting method.
The biggest advantage of calorie counting is it's more reliable than looking at the balance everyday because a ton of stuff will make you a few pounds heavier/lighter at any time it fluctuates too much. The scale doesn't move for weeks and people panic but really it was just random and then they lose 5 pounds on the 5th week and they think "omg, i must have lost all the weight at once because i ate that one apple!" You just can't use a scale short term. But all you have to do is count the calories, believe in the process, and if after months it doesn't work, you adjust your estimate of how many calories you burn and change your diet based on that.