Jumpers are like the shift key of a keyboard. Jumpers should be on while either powering on or while resetting power. That’s just a fraction of a second they need to be there. Once in recovery mode the jumper is no longer needed. Typically you would either:
Install jumper. Reset power. Remove jumper. You in recovery mode. Flash.
Install jumper. Add power. Remove jumper. You in recovery mode. Flash.
Once a flash completes the Jetson will automatically reboot. If the recovery mode jumper is still present, then I could see this as causing failure at the step of installing software. Quite likely the Jetson would go back into recovery mode instead of booting normally after the flash. This would basically be a successful flash followed by putting it back into recovery mode if the jumper is still there. It’s a bit like typing a document and accidentally having the “CAPS Lock” button on without knowing it. You’d never get the virtual ssh device because you’d never be booting normally…you’d be going back into recovery mode, which you do not want.
Note that serial console can be used to interrupt boot. Perhaps it was booting correctly the entire time, but activity on the serial port, or a jumper still being present, made it appear that it wasn’t booting correctly. Don’t know for sure, but those are possibilities.