Did you ran that command while the MOD Duo was connected to your PC?
DId it ask for a password?
Did it show a copy progress on the terminal? (like this)
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 18552 100 18552 0 0 46776 0 --:--:-- --:--:-- --:--:-- 46730
If you manually update the footswitch firmware, make sure to update the MOD OS version too.
The latest footswitch firmware needs the MOD Duo to be at v1.4.1 or v1.4.2.