Dear Sathysjit,
In short: no, you can not make ATK save the converged electrodes to the nc file before converging the full device.
If you look in your script, the "update()" function call is the one that instructs ATK to compute the ground state electronic structure of the device. This is followed by the "nlsave" call, which writes the converged ground state to nc file. So the full device calculation must converge before it is written to nc.
device_configuration.setCalculator(calculator)
nlprint(device_configuration)
device_configuration.update()
nlsave('myfile.nc', device_configuration)
Regards,
Jess