Late to the party as always, but: https://steamcommunity.com/sharedfiles/filedetails/?id=2751666316 This was my experience and I believe it happens, whenever a storm is raging with really high waves. Maybe if it slashes something it gets stuck there, or it just bugs up in the air in certain cases. Jumping onto it had it fall into the water again (sadly no flying boat for me). For my case there were no mods involved. Posted it back then as a reminder if you'll ever be searching for your boat and can't find it ;) Actually took me like 15 mins because it was so high up behind the house so I dind't see it at first ...