Full Idea
Thinking about the original ship as a ship, we think we continue to have the 'same ship' as each part is replaced; ...but when we think of them as physical objects, we think the original ship and the outcome of the reassembly are one and the same.
Gist of Idea
Thinking of them as 'ships' the repaired ship is the original, but as 'objects' the reassembly is the original
Source
Michael Jubien (Possibility [2009], 1.4)
Book Reference
Jubien,Michael: 'Possibility' [OUP 2009], p.16
A Reaction
It seems to me that you cannot eliminate how we are thinking of the ship as influencing how we should read it. My suggestion is to think of Theseus himself valuing either the repaired or the reassembled version. That's bad for Jubien's account.