I have a Boss FS-5U as well and was able to get it to reset the Harpeggiator.
I set the polarity switch to the right, connected it to my H9, went to the pedal setting in H9 Control under General Settings named 'Use Expression Pedal, Aux Switch or Both' and set that to 'Aux switch'. Then, I went into Aux Switch Mappings and set the Performance Switch parameter to 'Foot Switch 2 (Ring)'. Now, whenever I press the FS-5U, the H9s display briefly shows 'RESTART'.
