plex_scan.sh

#!/bin/bash
#probably needed to be run as plex user
export LD_LIBRARY_PATH="/usr/lib/plexmediaserver"
export PLEX_MEDIA_SERVER_APPLICATION_SUPPORT_DIR="/var/lib/plexmediaserver/Library/Application Support"

arg=$1

rtorrent_tv="/rtorrent/tv/"
union_tv="/union/tv/"

if [[ -f "$arg" ]]; then #check if it's a file
    directory=$(dirname "$arg") #return base folder if it's a file
else
    directory="$arg"
fi

#I haven't found a way to automate choosing library_id; the path replacement can probably be simplified based on your setup
if [[ $directory == ${rtorrent_tv}* ]]; then
    scan_directory=${directory/$rtorrent_tv/$union_tv} #replace rtorrent path with union path
    library_id=4
fi

"/usr/lib/plexmediaserver/Plex Media Scanner" --scan --refresh --section "$library_id" --directory "$scan_directory"