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I don't know that I'd be the definitive authority on the finer points, John. I don't use iOS devices, I'm still looking into a reliable Bluetooth dongle for Win8.1, and my laptop doesn't have MIDI DIN out (for the 'Connect MIDI Device to Eventide Device' option in H9 Control Settings). I have an H9, but the HarPeggiator algo work comes from my PitchFactor.
Disclaimers aside …
That's correct, if you mean a MIDI Clock coming in over the MIDI DIN plug. If you're plugging in USB to use H9 Control for programming (like I am), that takes precedence over the MIDI DIN jack input. The app itself generates its own competing 'internal MIDI clock'. You have to physically unplug USB from the H9 to gain back external clock (with Clock In set to On/Yes).
Without working around it … yes. When my main pedalboard is in the home studio, it's hooked up to MIDI pedal control, rack FX, a MIDI router, my desktop DAW, mLAN mixer, etc. I have selectable sources of MIDI master clock; each one fits different situations. So the easiest way to program my H9 and PF is to plug in a laptop via USB – *without* breaking the other routing connections.
So, I end up wiring in for H9 control programming, disabling the incoming MIDI Clock, matching the BPM in the H9 Control app, programming & tweaking the preset, removing the tether from H9 Control, re-enabling external MIDI Clock control, and integrating the preset back into my main system.
It sounds like a PITA, and it is. I still get caught with forgetting to reset some setting (such as closing H9 Control before removing USB – it gets lost and freaks out). But that's how I work around all of this. I tend to do the 'coarse' preset configurations with H9 Control, and fine-tuning on the H9 and PitchFactor devices themselves. It helps to have a lot of templates in my MIDI pedalboard geared to different algorithms.Show More...
The new Looper algo programming drives me a bit crazy, because it really *needs* to be integrated into the whole system while tweaking [MIDI Start / Stop]. The same goes for any rhythmic-focus algorithm (like the HarPeggiator). I'm still working on a better way to go about this, but for now … it's the best I've got. Programming in H9 Control still beats any of the earlier methods.