Which distribution are you planning to run?
See the Plex Linux Tips: Migration from another OS to Linux. Look over the rest of the document as well. It has some good info on running Plex on Linux.
You can run both servers at the same time. It will not cause account issues. Plex supports having multiple servers claimed by the same account.
Both servers should initially run the same version of Plex Media Server. This will minimize any database changes when copying the files to the Linux system. Once the Linux system is up and running, the servers can run different versions of Plex Media Server.
Give the Linux server a different name than the Windows server.
If you share media with others, you will not have to re-invite them. You will have to share the libraries from the new server with them. They will have to pin the desired libraries to their home page.
See Sync Watch State & Ratings. Enable it on your account. Have anyone you share with enable it on theirs.
