Obviously I don't know for sure, but I don't think it's possible for items to be returned to a bank box when the character is offline.
I do wonder if some adaption of the Magincia Warehouse function could be used to store the boat and its contents with a harbourmaster for, say, 90 days?
The difficulty, of course, is preventing people abusing the facility for free storage - so maybe the ship could be stored, but not the contents?
Well, considering the cost of the Britannian boat and the limit of 125 items I do not think that it would be much abused just for storage. Spending real money just to store 125 items through the Britannian's Hold when one can already use 7 characters' bank boxes and a house secures is not something I would think about, personally.
On the other end, by not allowing the Hold's contents to stay safe like the ship basically this would remain the annoyance to have to remember, for a ship that cost real money to purchase, to refresh the boat every now and then to keep the Hold's contents as safe.
And even if there was concern about that, just limit the capacity of the HaurbourMaster to hold as safe the limit of 1 Britannian boat per account per shard.
In my view, I would use the Harbour Master for this particular Boat (automatic storage after the set time for refresh) like the StableMaster works for pets (they get also stabled automatically on certain occasions...) only, that the Harbour master would work for the Britannian Boat like the StableMasters "used" to work for pack animals when they were able to be stored with their contents (not like now that they have to be empty).
So, I assume that the old code for loaded pack animals could be used with some adjustments for the loaded Britannian Boats and we would no longer risk having unsatisfied players losing their Britannian boats and its contents, a ship which they purchased with real money.......