I have done a similar thing in the past, but to flash firmware onto any device with a certain USB descriptor that gets plugged in. It was a mess of USB hubs and cables, but it worked.
What I did was write a udev rule that checks for the vendor and product id of a newly plugged in device and calls a script when there’s a match. The script then performs the flashing and logs the output.
In your case:
dd
the source USB to a file (make sure the partition you’re dding is smalled than any target drive- Udev rule according to your needs (all the same product or different drives?)
- Script that dds the file you created earlier back to the newly plugged in drive.
Edit. Did this on a rpi3
I recommend installing calibre web on a home server, installing koreader on the Kobo, and accessing your eBook library over your WiFi and OPDS.
Koreader is such a good reading experience, I never want to go back to stock firmware (well, except for the dictionaries maybe, those are better.)