Normally capacity helps set the charge rate. If the charger would time out/stop do to the capacity setting and not because the pack is full you should simply be able to start it again and it SHOULD recognize the CC/CV settings and stop when the pack is actually full not based on capacity...In my experience

My point, worry more about the CC/CV of the pack and charger than the capacity settings.

I can tell my Hyperion that a receiver pack is a 6000mah capacity but it will simply stop when it sees that it's full based on CC/CV and not the capacity I tell it.