Ok, a fair number of users have run into this problem. We've had a couple of H9s sent into us that show this problem, but we've never been able to reproduce it.
But in any case there's any easy work around. Please download the desktop version of H9 Control on either a Mac or PC, and update while connected to H9 Control via USB.
If you run into the same problem updating with H9 Control via USB, H9 Control comes bundled with an app called the Eventide Direct Updater; this updates the H9 using a different mechanism and this has always worked for users with this problem in the past. You can open it on Mac by clicking on the Window menu item in the Mac menu bar at the top of the screen, and you can open it on Windows by finding its shortcut in the start menu or by going to H9 Control's directoy under Program Files.