use the the trainer to change the item on slot 1 then send the ship on a expedition, now soon as he leaves the session go on expedition menu and call him back or wait the whole thing when he arrives the item should be usable, i did it with jack of all traits on slot 1 and he aways came back installed on the ship
What's your system OS? Windows 7, 8, 10 ?
No, was too a problem in other anno games. This Items work in some different way.