I’m wondering, unfortunately not able to test, if I delete a complete TV show and add it back to Plex later, will it still know that I watched season 1 & 2 but not 3 or will it mark season 1 and 2 as not watched?
Depends on settings (Is your Plex set to empty trash immediately?), how long it is before you restore the file, and whether or not you add it back to the exact same library.
Plex by default keeps media info (in case of network shares/USB drives being offline/etc), but cleans data once a week (I’m not sure of when/how it schedules itself, the options in Plex server settings only say ‘once a week’).
If the file isn’t there when the housekeeping runs, it will be reset.
Additionally, ANY change in library, with exception of a library title change, will cause Plex to see it as new.
(ie, you can’t move the file to a new library or folder without Plex seeing it as new)