I've recently started sharing one of my libraries with a friend, who is watching a TV series. However, as they're watching the series the episodes are being marked as watched, and therefore I'm losing my place on "On Deck" so I have no idea what the last episode watched was.
Is it possible to have it so that only the owner of the library updates the watched status, or even better, that status is unique per user?
It is the current normal (one deck per user) behavior if you actually asked them to register to Plex and shared your library with them instead of sharing your account.
Yes, I asked them to register with Plex then I shared the library. They aren't using my account, they have their own account. They seem to be updating my watched status of a series when they watch my content via the shared library.
The process you seemingly have to do is to delete each individual episode's view history on trakt.tv (there is no easy way to do it in bulk), then to mark it all as unwatched in Plex. If you only do one of these, the next sync will undo all your good work :(