I'm Actually having the same issue. When my H9 is on and paired with the editor I will adjust the parameters of the pedal such as selecting "Pre/Post" Routing and MIDI Clock settings. But I'm unsure how to save these settings within the H9 so that I don't have to set them up every time I power on the pedal.
The H9 should save all these settings when it is powered down. If it does not, make sure you are using the Eventide power supply. If you are, and it is not saving, this indicates a hardware fault.
Note that Pre/Post is configured and saved on a preset-by-preset basis.
You can check that things are being saved by loading a preset other than (1) and power cycling. The preset you loaded should be the current preset.