I should be able to control both from one H9 Control app, right?

Yes, you should be able to control both from H9 Control.  After updating, sometimes weird problems can occur;  resetting the H9s system settings oftentimes helps.  You can do this by turning your H9 off and then turning it on again with the right footswitch and the HotKnob switch pressed (the one in the upper left hand corner of the H9).