Regarding watched status, see Sync Watch State and Ratings. This syncs watched status with hosts at plex.tv. It is an account, not server, setting. Note the requirements listed in the support document. You will need to update to a newer version of Plex Media Server.
To move from another OS to Linux, see the Linux FAQ: Migration from another OS to Linux. This copies the entire Plex Data Folder to the new server.
Plex will still scan the libraries on the new system. You are adding a new folder to an existing library. Plex does not know the new folder and the old folder point to the same files.
