Server Version#: 4.8.3
Player Version#: All
This is a recent thing, so not sure if there was a change that I missed. Historically, Plex has removed episodes of TV shows from the library when they are deleted externally. If I watch the show outside of Plex, or decide not to watch them and delete that shows folder from my system the shows still appear in Plex even after a rescan and emptying the trash. The ‘parent’ folders have not been moved or changed in any way.
In the past, when I rescanned the content it would see that the episde(s) were missing and remove them from my library. Now they continue to show even after multiple scans.
Library options are set to scan daily (plus I manually scan as needed), empty trash automatically after every scan is checked (and I have manually done this), and allow media deletion is also checked.