Is there a feature that disconnects the Audya from it's front panel? Local off, I think many WS's called it...

Strikes me that that, combined with a loop through filter on vArranger might solve the issue.

I have to confess, I'm also not really keen on sys-ex over regular MIDI CC's and MSB/LSB codes for arranger functions. Longer sys-ex strings can interrupt the timing clock functions, and make the MIDI stream a bit jittery...

Both Korg and Roland do most arranger operational codes with CC's and PC's. Yamaha use a combination of CC/PC's and sys-ex. It's this lack of any standardization that makes hooking one thing to another fraught with problems. We really need the major manufacturers to get together and standardize this stuff...
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An arranger is just a tool. What matters is what you build with it..!