Calm down ...Your boat ( Ship ) is not lost!
It is just where you left it.
I swear even Captain Morgan doesn't drink so much rum he forgets where he parked ( docked or anchored ) his ship.
Just use another character put in a small ship ( very cheep now ) and go out to where you left your ship and remark rune. after checking that it works. sail the small ship to the nearest land and dry dock it.
Until this bug is gone for good I would suggest that you anchor by a safe spot on shore, hop off and mark a rune on land, This is what I do.
So today when my rune to my ship didn't work ...no problem.
I did get lucky in that it only hit my fishing Ship today.
I was able to recall to my ship at the floating docks.
Also NEVER recall off your ship in mid ocean without jotting down a sextant reading.