So there's a Sonos feeding the Yamaha and a Sonos feeding the multi-room amp? Or one Sonos Connect feeding both the Yamaha and the multi-room amp?
If it's either of these elements, then no, the issue sits with Sonos not outputting in-sync with itself. If you connect the Zone 2 pre-out to the multi-room amp then yes, you can fix it by selecting 'audio sync' in MusicCast. If you can't... then see point above.
This industry is not getting cheaper and cheaper, we're simply convincing ourselves that we have to push the cheapest option to customers. #makesonosgreatagain