There's a new version of H9 Control out that should auto reconnect properly to an H9 when connected via MIDI. It also has support for Bluetooth on Mac OS X and Windows. So, instead of connecting over MIDI, you could connect to your H9 over Bluetooth on your Mac by going to the Devices menu in the Mac menu bar and selecting "Connect via Bluetooth".
http://www.eventide.com/AudioDivision/Support/Stompboxes/H9.aspx
