Wasn't the point of the Ship of Theseus precisely that establishing wether something is or isn't something else is at least complicated? Using it right after saying "X is still Y" kind of seems to make the opposite point.
Similarly, a "fork" as we understand it in the context of software is this thing that, even though it's a modified copy, retains its extrinsic identity: "This software X was worked on in Y context, and is now being worked on in Z+ contexts". Same software, even if it gets a name change.