This all sounds too complicated to use live, although one possible scenario might make it do-able...

Can the Yamaha transmit Sys-ex from an arranger Part? You MIGHT be able to do a sys-ex dump of the Sonic Cell's current state (including Part mutes and effects routings, even the patches used), and then put that at the start of each Intro (usually, a blank bar is sufficient to transmit it and avoid glitching) and thus avoid touching the SC before you start.

Is this possible?