Isn't there an option to delete only from the library?

If there are folders or files that are deleted from the disk when plex-media-server is not running, when you turn it on those folders remain in the catalog and I don’t see any option to delete those contents from the library (on the disk they don’t exist anymore).
There is an advanced option under “Library” option to delete files from hard-drive but that option is unsafe in this case.

We’re all hoping (especially me) this works:

Expand Sidebar/More/‘The Dots’/Manage/Empty

Good Luck.

Scheduled Tasks can ensure that happens during maintenance - but is that what you want? You decide.

If you refer to ‘Empty Trash Automatically’ as unsafe - you are correct. It certainly can be.

If you bring up the movie, click the 3 dots and get info.
It should show that file is unavailable and allow you to delete that one file from the database.

same thing if you make a change to the file name then Plex shows 2 files.

Ok, but in the case of a TV show, you have to delete it episode by episode. There should be a simpler and more direct way to do it. After all, deleting from the library is not irreparable as it can be added again.

You can remove a whole season from the Server

That depends on your settings and what your system does to files Plex Deletes.

IF you allow media deletion Plex will, in fact, remove that file from the file system. IF the file system puts that file in the Recycle Bin, that’s cool. If it doesn’t - it’s gone!

Some clients don’t allow the removal of entire seasons or shows - some do. I’d like to be able to do it - with the proper warning.

The Setting: Empty Trash Automatically on every scan - is NOT recommended for systems that allow storage to sleep, spin down, go missing, or change Drive Letters because it’s a real PITA when Plex removes items from the database when they go temporarily missing.

Those files are NOT removed from the file system, but the PITA of having to re-index them all - is real.

If you meet any of those criteria - keep that setting disabled.

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