If you get that problem on a clean install, then that suggests you have a problem with plex, not a problem with reusing a previous library.
I don't see how that could be a problem. It would just mean that plex.tv wouldn't know about that server. I don't think it should be a problem creating a new server at plex.tv
I don't specifically remember removing any, but I probably have, since I have had plex server on a number of different platforms over the years, and the only plex server I currently have is the one on my Unraid (and it was originally a needo docker as you know).
If you are still in doubt, you might see if anyone has anything to say about removing a server over at the plex forums.