What software do you have installed on your H9? In earlier releases it wouldn't save those assignments immediately but instead would wait until the H9 was turned off. And sometimes the H9 wouldn't have enough power remaining at power down to save them correctly. In more recent releases the H9 is saving those MIDI mappings immediately. Do you have the latest release 5.0.1 installed? You can find out what you have installed by clicking on Pedal in the bottom bar of H9 Control and going to 'Update Stompboxes Software'.