That's just like saying that an ice-axe is its handle - what if you replace the smaller "important" bit of ship piece-by-piece?

The quintessence idea is more interesting, however. We could think of an item's quintessence as being removed by damage, and slowly recharging with experience - if the new mast survived many storms, say, it could grow to be an important part of the ship in its own right. However, if too much is removed at once the ship's quintessence drops too low, and it can no longer be considered the same ship.

Energy - are you aware of

Noether's Theorem? Essentially, symmetries of a physical theory are in one-to-one correspondence with conserved quantities. Conservation of energy is equivalent to time-invariance of Newtonian physical laws, conservation of momentum is equivalent to position-invariance, etc. Of course, it's more general than that, and holds in non-Newtonian cases - I believe conservation of the stress-energy tensor is given by Noether's theorem and relativity's invariance under diffeomorphisms of spacetime. But this is way beyond my actual understanding of either Noether's theorem or general relativity.