Will a scheduled episode (say it is set as New and Repeat Airings) mark an already episode as unwatched?
Ideally, I’d like an option to only record episodes that I don’t already have on the server. Is that an option?
If you already have an episode in the same library that the DVR will record a series set as New and Repeat scheduled Plex will not record the episode.
Image below shows Program Guide with Season 2 Episodes 12 & 13 airing over the next two Tuesday nights. Recording setting for Show set to “New and repeat Airings.” Recording Priority showing no upcoming airings to be recorded because the two shows are currently in the same library the recording is saved to.
If your already recorded content is not in the same library as the DVR records to then yes you will always get the same episode recorded over and over again.
ok, good 
Follow on question – if I set the program to delete episodes after watching, will it record them ?
If the episode reairs in the future and is not in your library then yes more than likely it will.
