Hello pecabo,
Absolutely nothing has changed in Hauptwerk v6 above v5 related to ranks or audio routing; the act of upgrading to v6 definitely couldn't, in itself, have changed or broken any audio/rank/routing settings or behaviour in Hauptwerk.
However, note that some audio interfaces (notably some from RME -- not sure about the Babyface) do present less usable audio channels if running at 96 kHz. Hence if you had set Hauptwerk v6 to use 96 kHz audio and you were previously using audio channels on the device that its hardware/driver can't use at 96 kHz, then you wouldn't hear sound that was routed to those 'missing' device channels.
If you've set Hauptwerk v6 to use 96 kHz audio, then try relaunching Hauptwerk (so that the audio interface's channels are re-queried). If that doesn't solve it, set Hauptwerk's sample rate back to 48 kHz, re-launch it, then see whether that solves it.