Welcome, David.
Your problem is, the calibration instructions apply to the Atmel front end, which is the “emon” part of the emonPi, and it’s totally separate from the Pi part, the two communicate via a serial link.
You need to compile the source either on your computer or on the Pi, find the compiled .hex file, then upload that via the serial link.
https://wiki.openenergymonitor.org/index.php/EmonPi#Uploading_Arduino_Firmware
for the instructions to do that.
But even when you’ve done it, there’s a big danger that if you update emonCMS, you’ll overwrite your calibrated sketch and lose your work.
This is why I always recommend adjusting the "scales = " line in emonhub.conf.
When/if you do update emonCMS, choose the “wrong” option, in your case choose “emonBase”. That will try to communicate with the Atmel at the wrong baud rate, and fail - which is what you want.