The Ship of Theseus is not a parable. It doesn't have a lesson you're supposed to take away from it. There are different of ways of looking at the problem. The "solution" that appeals to you is probably a reflection of how you think, but there isn't one "right" answer.
For example, one answer is to look at the ship as a 4-dimensional object (the three spatial dimensions + time). Yes, the material in the 3D slice at t0 is different than at tN, but you're still looking at slices of the same object.
For example, one answer is to look at the ship as a 4-dimensional object (the three spatial dimensions + time). Yes, the material in the 3D slice at t0 is different than at tN, but you're still looking at slices of the same object.