this happened to my ship and i found a fix, not an easy one
what i did was have two guild mates push my ship with me on it into range of the colussus, wont move without me on it. They drew a flag ship as close as possible and i disabled it. Now when i defeated the ship and went back to my ship it was still stuck BUT when I let the crew kill me and sink my ship, it reset for me.
I also fixed a guild mates ship by taking out a light sloop and luring a MOW over to his, I hid behind his ship while the MOW fired on me, it hit his ship instead and sank it. Not easy to do because it seems that the stuck ships are invisible to enemies, a small ship needs to hide behind the stuck ship for it to work.
If anyone needs me to help them unstick their ship just send me a PM.