The latest desktop builds of H9 Control — v1.5.3 — will let you save presets in a preset list in bypass and download the preset list to the H9 in a way that preserves their bypass state. We submitted a new iOS build with this feature as well to Apple, but it usually takes them a week to approve things.
You can download the installers for H9 Control v1.5.3 here:
http://eventide.com/AudioDivision/Support/Stompboxes/H9.aspx
