If the controller operation is intermittent then it could be due to a dodgy wiring connection somewhere on the harness.
If the regen has been accidentally set to zero in the software, it might also explain why it is not working.
But, if you are still convinced that the controller itself is causing the problem then changing the controller is a relatively straightforward job, as long as the fixing bolts for the controller and the cooling fan/disc mount come undone OK.
I always use a good quality Allen key to reduce the possibility of the tool slipping inside the hexagonal sockets in the end of the bolts as they can sometimes be very tight.
Check out Gary's
Magic Pie III Controller Swap video to see exactly what's involved.
Regarding tha battery damage question, if you are using a battery pack without any
BMS protection that is only able to accept a low charge current you might damage the battery by using regen at high speed as the charge current produced by the regen may be too much for the battery.
If two of the 5200Mah Multistar LiPo packs shown above were wired in series, the 29.6V 5.2Ah battery would have a continuous discharge rating of 10C
(52 Amps) and a 10 second peak discharge rating of 20C
(104 Amps), but the maximum recommended charge rate for this particular pack is only 2C
(10.4 Amps).
Two
(or even three) of these packs wired in series would be unable to cope with the regen current from a Magic Pie.
When I last measured the
regen current on my Magic Pie 4 it produced just over 26A at only 20 mph.
Alan