Short answer first, then the reasoning. There is also a quality change that the scan cannot see. Weight loss shifts fiber-type distribution toward Type I and improves mitochondrial density and insulin-stimulated glucose uptake per fiber — so the muscle you keep is metabolically better even though there is less of it. That does not make the loss irrelevant, but it explains why function often holds up better than the number suggests.

InsuranceTom said:

There is also a quality change that the scan cannot see.

Right, and protein targets should be set on a reference weight rather than current weight. Setting 1.6 g/kg on a starting weight of 130kg produces a target nobody hits on a suppressed appetite.

FitDadDave said:

I lifted three times a week throughout and still lost lean mass.

Can confirm the pattern FitDadDave describes. The intervention that works is boring and well evidenced: resistance training two to three times a week at a genuine effort, protein at 1.4 to 2.0 g/kg of reference body weight, and not making the deficit larger than the training can support. Cardio does not protect lean mass and in a deep deficit competes with recovery.

Clinical perspective, offered as context rather than as advice.

Sharing my comprehensive lab data relevant to lean mass:

Protocol: Semaglutide 1.7mg/wk, resistance training 3x/week, protein 1.2g/kg/day.

The improvements in lean mass are clearly reflected in these numbers. The inflammatory marker reduction (hsCRP) is particularly striking.