It is the opinion of a knowledgeable friend of mine that Koetsu just sends you a new cartridge.
I’ve had a couple Koetsu stones rebuilt. They definitely reuse the old body and (usually?) the magnet. Everything else (armature, coils, damper, suspension, yoke, cantilever & stylus) is newly built. And they do a great job of it! Consistently great results. Maybe on the "Black" model they replace with a new one, but I couldn’t speak to that.
I believe Ortofon also takes this approach, though I haven’t had one rebuilt yet. Their info site on rebuilds used to warn that your body could come back with scratches from the work.
In both cases the "full rebuild" runs around 50% of a new model, sometimes a bit less. Koetsu won't penalize you for having the premium stones - rebuild cost is the same for any stone, though the diamond cantilever upgrade is quite costly if you opt for that.