Only thing I can think of is using the WET/DRY routing option on the H9. But you would need to setup up two presets of each effect:
One presets would be in STEREO mode for full effects (the ACTIVE state preset).
The second would be saved with WET/DRY 2 and a MIX level of 0 (the BYPASS state). The dry signal would come out of ouput 1 and the wet signal (which has a MIX of 0) would ouput nothing on output 2.
This sounds very tedious to incorporate for all presets and wouldn't work for most MODFACTOR algorithms since most don't have a mix control.
I hope this helps!