The obvious counter-example comes from the intermittent fasting literature, wherein adipose tissue loss occurs even when the net calories consumed in the IF diet are
higher than in the ordinary diet.
Another vastly replicated result you can find quite easily: low-glycemic-index diets and ketogenic diets can produce weight loss despite caloric excess.
And lastly, a reasoning from first principles reveals a prima facie credible flaw in the caloric balance hypothesis: the body is not a closed system, ergo the law of conservation of energy does not apply. More vulgarly: you can do things like "work up an appetite" or "shit excess food".
Google Scholar is positively littered with relevant literature, so I'm somewhat surprised by your skepticism. Good key words to enter are: "carbohydrate-insulin model" vs "energy balance model". The carbohydrate-insulin model is also credibly debated, of course, but the question of whether this is the right alternative is distinct from the question of whether the energy-balance model is correct.
In no specific order, here is a pair of completely arbitrary papers, intended only to show that relevant papers can be found with minimal effort:
- https://www.sciencedirect.com/science/article/abs/pii/002604...
- https://academic.oup.com/ajcn/article/115/5/1243/6522166
I'm not objecting to the energy-balance model, which may well be correct in an important way. I am merely pointing out that nutritional science has not managed to reach consensus on this fundamental issue.
>These have all have nutritional studies.
The nutritional studies did not produce these initial findings. Without pointing to specific papers, it's hard to be very precise, but I would be willing to bet that these are either dietary studies building off of biological first principles, or replication-checks in broader studies. Both are totally fair practices, but can't be considered as an indication that nutritional science is a fruitful field.