The first time it was moving, but if it had continued to move I'd expect to find a wreckage as it was near rocks. The second time however it was not moving, I was anchored near an island. If the boat still exists, but simply floated away, shouldn't it appear on my map?
If you lose connection to the server while out to sea, upon rejoining the server you will be teleported back to the start gate. The boat will remain on the map, but if you return to the area where the boat should be, it will be missing. Happened twice in a row.