The BYPASS won't remotely work if it's not patched to an external controller, being it a footswitch, a pedal or a MIDI CC message.
If you press SETUP 3 times you'll see an EXTERNAL menu. Press its key, then the SETUP key again, a few times, until you see a BYPASS menu. Here you can patch an external device to your Eclipse BYPASS. If this hasn't been done, the BYPASS won't be remote controlled.