Bonjour Jean,
You're saying that by switching to 96kHz only 1 out of 4 channels is playing. I presume that at 48kHz all 4 were working then. If you reverb back to 48kHz are your 4 channels back? Have you checked your physical connection and your surround amplifier settings. Some has surround processing modes who can change the audio result. If it is a Home Theatre amplifier/processor/receiver then we usually select "Direct mode" (no processing) for Hauptwerk.
Switching sample rate doesn't affect the audio routing. I have no idea of the interface used in your console. I know that some will have limitations (less channels) when increasing the sample rate, but from 4 to 1 I would be surprised. From 4 to 2 would make more sense.
Can you confirm that reverting to 48kHz brings back all your channels? Do you know the brand and model of your audio interface? You may want to send me a diagnostic file (In Hauptwerk go to Help | Create a diagnostic... and email it to me at support [at] hauptwerk.com