I opened the newest version of the project in safe mode. It asked if I should open one plugin, I clicked no, and it opened without plugins. But the mute and pan assignments are back.
I generally save [project-date-version] so with this song, appropriately titled "Trouble"

I'd save it Tro_08-18-14 to two separate external hard drives, make changes, save it as Tro_08-18-14a, Tro_08-18-14b, etc.
I generally don't use a lot of plugins unless the individual tracks need EQ -- these were mostly EQ. I might have one or two delays and maybe a reverb on separate stereo buses and use the channel fx sends.
I strapped a PEQ5B across the drums bus and it's working. I have a feeling X3 doesn't want to work with mixed and matched batches of plugins. I have to stop working now but so far I like the Nomad EQs and delay better than the Cakewalk or sonitus ones for this project so if they work I'll ditch the old plugs and move on.
Which brings us to automation. I don't think that's going to be a big deal -- I've mixed this track a couple of times before. The biggest automation problem I've had is while comping takes when I can't do crossfades; one track has to be muted as another is unmuted. It was tricky, and hard not to wind up with an audible click or two. I'm keen to try out the new comping tool. It looks like it will save a lot of time and... trouble.