The beginning of the article linked says "if you usually consume 2,500 calories a day and then cut back to 1,600 calories, you’re going to lose weight from that 900-calorie daily deficit — even if all you ate was potato chips. But you won’t be healthy and you most likely won’t be able to keep the pounds off."
I went from 245lbs to 185lbs by eating 1500 a day every day for 5 months, that was over a year ago and I still weigh 185lbs, all I did was when I hit my target weight was make sure that over a week my diet averages out to 2500 a day, some days I go over by a few hundred, the next day I just under eat by a few hundred so that it balances out.
It isn't so much that calories in/out is false, as the equation of "calories eaten - (activity + bmr) = weight change" that is false. The food you eat has a massive impact on your biochemistry (and thus your metabolic rate), and microbial metabolism also varies significantly depending on the substrate you provide them.
