Hi and
to the Forum.
I'm pretty sure there isn't a manual specifically for the Fly 600, but I guess the wiring will be the same as the standard Magic Pie kits.
I'm assuming it's just the power cut-off and regenerative braking that's not working, rather than the mechanical brakes themselves.
Anyway, it sounds to me as if you may have an intermittent connection on one of the thin black ground wires, as this would definitely cause the symptoms you've described. Check all of the wiring harness and connections carefully and see if you can find any signs of damage, or loose/broken wires.
Take a look at
this post for more details on the Magic Pie Wiring.
Alan