Ok, so on the server I admin everyone made a new character and company, invited me to them, and I got all their stuff back with the commands. Easy enough and everything seemed to be good. Today, after a server restart I can not see the majority of our company's beds again. I can't see any on any ships. Fyi @Jatheish
Edit: The only bed that was working was one of eco's beds (Her two mods--RP decor and Atlas foliage--and unlockable submarines are the only ones we have on the server.) Picking up her bed, demolishing the simple ones, and replacing with vanilla ones only worked for land based beds. Ship beds still do not show up, although I can fast travel from them.
Edit 2: The previous trick of one person leaving the company, making a new one, and the remaining members merging with the new one worked again as per before the attempted fix. Given today's experience though, I don't have confidence it will persist past a restart.