Problems with a 36V backup battery

This is a friends efatbike. He used a 36V hoverboard battery as a backup, reducing the cutoff to 30V on his controller display, no problems and it lasted an amazing 8 miles at full throttle. Put the original 48V battery in and now it cuts out on takeoff, you have to feather the throttle till it reaches 10mph, then you can give it full power. It sometimes comes up with 21 error, which is unusual current detected. Tried another battery same thing. Very strange...has the 36V battery damaged the controller? Seens unlikely, though something has happened.

My guess would be more likely the 48v battery is now weaker, but nothing to do with the other 36v battery. Sometimes effect has nothing to do with the last thing you did. Its just that the 36v battery was tried just after he killed his 48v.