While I don't have that exact charger I do have two Hyperions.

The mah setting will set the charge rate by default. 6 amps in his case. The only way the pack won't charge fully is if it's discharged to the point that it would take more than 6000mah to fully charge. IF the pack is say half charged it will charge until the cc/cv says it's full, regardless of the capacity of the pack.

IF the pack is drained close to LVC voltage and it may take more than 6000mah to reach full charge, and the charger stops at 6000mah, simply start the charge process over again and it will charge to full capacity.