Disable the setting in Plex to automatically empty trash.
With that setting enabled Plex is deleting the media from the database as soon as the file is deleted and before the new version is written, causing it to appear as newly added.
Disable the setting in Plex to automatically empty trash.
With that setting enabled Plex is deleting the media from the database as soon as the file is deleted and before the new version is written, causing it to appear as newly added.