I requested a list of commands. Never suggested a factory reset, but now that the pedal is basically reset, try this:

In the system settings > MIDI >  MIDI – Global control, assign a CC# to P act/byp (M).

From your Boss switcher, you should be sending that CC# along with a value of zero for bypass or 127 to activate. Make sure you’re sending on the same MIDI channel as the H90, the default is 1.