Hi
you can not do upgrade from usb port this is a serial managment port
you could check if partner firmware upgrade is enabled
and see if you re-insert the controller with a problem if the controllers will update each other
in CLI
set advanced-settings partner-firmware-upgrade enabled
or try
set job-parameters partner-firmware-upgrade enabled
these command are from HP P2000 G3 MSA System
CLI Reference Guide
http://h10032.www1.hp.com/ctg/Manual/c02520779
Regards