Currently have 2 of the BlueSolar PWM-DUOs rigged up in parrallel, so each one has a connection to battery bank 1 output and battery bank 2 output.
Is it acceptable for bank 1 and 2 to have different Ah capacities?
Specifically 10Ah 24V on one and 32Ah 24V on the other.
Not ideal. Whichever battery finishes charging first will be maintained at absorption voltage until the second also finishes charging. This will lead to a shorter service life. If you reduce the absorption voltage settings to the minimum for those batteries, you'll have less life reduction.
