The difference is that The Ship of Theseus had all its parts replaced one by one, in a long period of time. If you replace 90% of the ship at the same time (RAM, CPU and Motherboard), then the analogy breaks down.
I didn't say it's not understandable, just that it breaks down - i.e. doesn't apply anymore.
The point of an analogy is to point out how our intuition tells us it's the same boat, despite having no parts in common with the initial boat.
As other comment mentioned, if you keep the sails and rebuild a new boat around it, no person in their right mind would feel that it's the same boat. It's very clearly a new boat, and the analogy breaks down.
