That already exists: left handed sugar.

Basically: some molecules can be constructed in two different ways that are mirror images of each other. It doesn’t really matter which, but it has to be one or the other. These are called left-handed or right-handed.

Normal sugar, produced by plants on earth, is right handed. Our bodies are built to metabolize right handed sugar. They cannot process left-handed sugar.

Chemically it is exactly the same as right handed sugar, the same structure only mirrored. It also tastes exactly like normal sugar because it is just sugar. It has no ill effects as not even the bacteria in our gut can do anything with it (so it doesn’t cause gassiness).

It is basically the perfect calorie-free sugar alternative. The only problem is that it’s super expensive to make, as nothing on earth naturally produces it.

With a replicator that wouldn’t be a problem; so I imagine they just use left-handed sugar.

And it’s not just sugar either, it’s basically everything. So you could set up the replicator to your desired calorie intake for the day, and then have it produce right-handed molecules until you hit your calorie limit and produce left-handed versions after that. You could eat as much as you want, not gain any weight and not even notice.