This is for new media eg --scan --refresh --section 2 --directory /path to new folder/ is the way how plex library scan works. Unfortunately Plex does not support scanning file directly only folders.
I was just thinking today, it would be nice if new media was refreshed to grab metadata, but it’s pointless to refresh anything which already exists, like adding an episode to an existing series/season. That’s just introducing needless file reads. Maybe in our scripts, we can add a check to see if the series folder or movie folder (perhaps using the “Series_Path” arguments. If the directory exists within the acd mount, run the scanner with just the scan flag. If the directory is absent from the acd directory, add the refresh/analyze flags. At most it should only ever be refreshing/analyzing one item then, and only new ones.