I've just had a similar issue but the other way round. The game autosaved, then a few minutes later I had a power cut.

Power comes back on, reload the game. My character is now back at base, but my ship isn't there, so is evidently somewhere in the ocean. There seems to be an inconsistency with world saving and character saving.

I had not the same issue but I really suggest you to avoid logging off while aboard.

The only issue I had, time ago, was when my connection was extremely unstable, so I "got disconnected" (which is nearly like to log off) while sailing into a friend's server: when I logged back into Valheim I found myself swimming (the fact I was not that far from the shore, together with some Black Forest rocks, saved me from drowning): later I used a raft to locate my drakkar, which was not that far from the point I was sailing when "falling overboard".

As far as I read, boats "stop moving" (like they was moored) as soon as they have "no player on them"... but, if they're moving when you log off, it could take some time for them to stop.
Also, if you're playing into a multiplayer server (which then remains active after you log off) some friend could always sail away with your boat (or just move it nearby).

Last but not least, thinking to the reason a boat can "disappear", it could be your server (or your PC, if single-player map) is using a backup-save from before the time you deployed that boat, I can think to nothing else, about the "disappearing" event (apart the boat being destroyed, and sunk, by a troll or such).