Maybe I'm misunderstanding, but I've run into this Catch-22 before :
You have a system actively assigned to an SQK. However, all the groups inside that system were locked out / inactive during the software upload. Or, you accidentally lock out all the groups via GKQ's via keypad.
After the upload, the SQK doesn't seem to work for that system since there is really nothing to toggle on! (all groups inside the system are locked out).
Trying to manually toggle the system's groups back on via the menu system/group programming structure doesn't seem to work, although it will allow you to go through the motions of making sure the groups are unlocked - but still the SQK seems dead and groups still inactive.
The only way around this in the field is to not use the menu structure for group restoral:
Hold the FN key long enough to make it "sticky". (if you are slow like me)
Rotate the knob and find the system of interest.
Now toggle at least one of the groups on via keypad, hit scan, and you are back in business.