To use any subscribed ship create a new world and select all workshop ships by pressing button Settings -> Custom Islands.
Select ships here.
Then enter new world and despawn your current ship (from inventory last tab ("I"-key menu "Spawn Home Island")) then spawn any workshop from "custom islands".
Save that new world, quit to main menu and reload you main world, despawn your 1st ship and then summon custom.
Then you will be able to have access to your both ships at that world save (but not all at once - only one of them) with all their loot.