I had the same issue. I didn't want to create a company, so I sailed back from Freeport. I destroyed my old beds and put new ones, they all work except for the ones on boats which still don't show up. And I still cant see my boats. Basically I'm stuck at home, cant risk sailing anywhere.
Edit: they patched again and the same thing happened, had to destroy all my old beds and make new ones. This is getting annoying.
Edit: I built a Brig and now I can see it on the map and put a bed on it and use that bed. But I still cannot see my older ships nor can I use beds on them. I might have to junk them and build new ones if they don't fix it.