There are a lot of possible hormonal problems that can cause this, so the answer is going to vary depending on what’s going on.
But broadly speaking, these are either going to increase your appetite – making you eat more, thus taking in more calories, or, they’re going to decrease your physical activity by tiring you out – making you burn fewer calories. Or perhaps both.
It doesn’t change the fundamental nature of the physics, yes, the calories have to either come from some where, or fail to go somewhere. What those hormonal changes do is alter your behavior to cause you to act in ways that are likely to increase your weight.
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