The exact same problem happened to me 3 or 4 months ago. My situation was a bit different from yours though, the following is all I remember and GMs can actually fix it.
I was on the Corgul's floating island with my boat being deployed on the shore(mine was not dry docked), I was busy fighting Corgul and didn't notice when server went down for regular maintenance. When I logged back in after server was back up, I saw my screen all white like it's flashing for a second and then I found my char standing near Gazer room in Shame, very weird, like my char was teleported to a random location. And then I found myself in the exact same trouble as yours...
I paged a GM three times, no response for the first page, paged again a few days later and got a response but I already logged off so I couldn't receive it, and finally for the third page, a GM responded to me very quickly(took only a few mins). I explained what happened to me, he said he's looking into my char's boat record/data(something like that). He said it seems my boat is still remaining somewhere and if he deletes it I could deploy a boat again so I said to him please do it.
After he deleted my boat, I could actually deploy a boat again(I just dry docked my new boat because I wasn't going to use it at the time), problem solved... I just appreciated his fast response and was happy that I could fight Corgul again...
BUT, the issue wasn't fixed actually. It just happened again after a server down the day the GM fixed the issue for me. I just couldn't deploy a boat, again, the trouble still continues... But I didn't feel like paging a GM again, I just gave up and left the problem as it was because I think it's a flaw in the code and probably beyond GM's ability. I just let my alt char to deploy a ship and let my main use it...
I think you should just keep paging a GM till they respond, they can fix it and you will be able to deploy a boat again... at least for a day though. My suggestion is that if you can successfully deploy a new boat after a GM fixes the issue, do not dry dock it (unlike I did) and leave it deployed on the water through server down and see what happens. I hope the devs look into this. Having a char permanently disabled to deploy a ship is definitely a serious issue. (The alter not taking certain maps, timer on the map sometimes doesn't start from full 2 hours and this boat problem... Corgul encounter seems to have been buggy since it's introduced.)