The recommendation about unchecking “Empty trash automatically” is based on one of the root causes why Plex might loose manual edits in general (incl. manually assigned collections).
If you have configured your server to do automatic or scheduled scans of your libraries (e.g. to search for newly added files) it can happen that Plex removes existing items if it can no longer find the underlying files. This can be about files on a drive that’s not connected to your server at that time or files on a drive that’s just too slow to spin up (making Plex believe it’s not there).
With the “empty trash automatically” option enabled, Plex will delete items it no longer finds in your library. Therefore… if your disks might not be connected at all times or might be slow to react, it’s good to disable that option.
When Plex rescans the same library again after such an incident, it’ll re-add the files (assuming the drive is connected / fast enough to spin-up) – however your manual edits will no longer be available.
If you disable “empty trash automatically”, Plex will keep the library record. There’ll be an indicator that this file is currently not available (trash icon) – however, the important thing is… if the record remains in place, so do your manual edits!
Side-note: that’s got nothing to do with Plexamp… it’s just how your Plex Media Server works and will affect all clients.
