Sorry – I still am not sure I understand.
As far as I can see, your problem is that you are controlling two H9's, one on MIDI channel 1, the other on MIDI channel 2. The channel 1 unit works as you expect, the other does not.
Assuming that I am correct, here are some possible causes:
1) I can't find any information on a Boss SS8 – I assume you mean ES-8. This is a complex unit and it is quite likely that it is not set up correctly – you should contact Boss for support.
2) If you are connecting BOSS -> H9 -> H9, this may be the problem. Try connecting the Boss directly to the second H9 and see what happens.
If this then works, reconnect and try setting the first unit first to MIDI/OUTPUT=THRU, then MIDI/OUTPUT=MERGE.
If it does not work, the problem is probably either the Boss or your cabling.
3) If these are not helpful, you should contact our French "Brand Ambassador", firstname.lastname@example.org