No.

Let's take the more direct approach and move the ship entirely and replace it with a copy.

Have you stolen the ship?

I suppose legally you could argue you haven't. The registration etc still applies to the customers ship, and unless the customer could demonstrate some kind of emotional attachment, there would be no 'loss'.

It's like going to a shop, selecting a tin of beans, when you pay, the cashier swaps it for another tin of beans. Have your beans been stolen?

Something something no-cloning theorem prevents this (/s, since of course, we could 'teleport' the ships's quantum state onto the 'new' ship (/s)).