The reason you loose the files in /mnt/downloads is because these files are not stored on your harddisk, but on volatile ram of the asus itself.

Thus, unless you save the torrents to flash (which makes no sense, since you have a harddisk/usb drive) the files are lost when you reboot.

Thus i recommend to put the torrents on /tmp/harddisk/torrent.

Check the settings.json file and change it to this setting:

"download-dir": "\/tmp\/harddisk\/torrent",

If you would like an alternative location, you can also make a subfolder
in /opt (which is normally the same as /tmp/harddisk).