It should be OK to use 20Ah in place of 12Ah batteries. 12V 12Ah battery compared to 12V 20AH is basically just a little bigger gas tank (so to speak)
If anything, you may be more likely to get motor a little hotter (due to longer run time)
I believe the 21A current limit you mentioned earlier is actually:
...the under voltage limit
...which means that your controller will shut down when your battery pack gets below 21V.