Yes, but it's a massive and complex feedback system. So every replaced piece is tuned back to be a good to perfect replacement - including thought. When that do

Yes, but it's a massive and complex feedback system. So every replaced piece is tuned back to be a good to perfect replacement - including thought. When that does not happen you get hallucinations or cancers, for example. You could build an empirically accurate copy of the ship in this way - not perfect but very close.