on my mimaki JV3, you have the option to select 12, 34, or 1234 (as in printhead #'s).
BUT I do ink fills all the time on a single head by simply disconnecting the hose above the pump for the channels I don't want to run.
I'd imagine you could do the same, no prob. The printer thinks its running its normal cycle, but its really only drawing ink through the lines that are still connected to the pump.