Bjørnssp wrote: There is no reason, for me, to assume that the codes sent by the Arduino for F# and G in octave 3, are not the correct ones since it is generated by the same sub routine as for the manuals.
This is almost certainly true, but you could check it outside of Hauptwerk by using one of the (free) MIDI monitor programs to look at what is actually being sent by the pedalboard and encoder. I use 'Bome SendSX',
but there are others. If the encoder sends the right messages when you press and release the F# and G pedals then all is well.
However, using the St Annes organ in Hauptwek you still won't hear anything as others have correctly explained. To rephrase the advice already given, in the hope that it may make things clearer, you need to remember that pressing a pedal doesn't generate a sound of itself, it just sends an instruction to HW asking the software to play the sound of that note
if it can.
The St. Annes organ doesn't have the top F# and G in the pedal divison, so neither does the HW version of it. Pressing or releasing either of these notes (on your pedal board) will send the messages to HW asking it to turn these notes on or off, but since the notes don't exist in St Annes, HW can't oblige and simply ignores the request.
You hear no sound because there is no sound to hear (for this organ anyway).
Nick