A few set backs and a few solutions.

Quick background - I have 3 files that I'm referencing. The flamingo, the chickadee and the garden (including any props).
I have 30 scenes. The referencing has been working well, until today.

Everything was working peachy keen. I updated my model and texture, had a smoothed version of it, made my blendshapes, created wraps, and it was all working nicely. I swapped out the old file with this new, updated one, and it worked beautifully as a reference file - EXCEPT for a few pesky CVs that didn't like to be scaled (50% ). If I were to do it all over again, I'd have made characters so wouldn't have to be scaled, but it's just too late in the game to change that. I'm sure there's an easy answer, somewhere in the wraps or weighting, but the easiest thing was to NOT scale the model BUT just scale up the set and props (200%). With this change, everything works. They're not ginormous, and the info isn't all that complicated. Just a time-wasting PITA.

I figured it was just easier to start with new, clean files and fresh references. The down side is that what little animation blocking I had done won't be used. The upside is that I had only done very little AND all the testing, experimentation, camera angles are pretty much set, as well as the timing and number of frames.

The upside is that everything is working. I can animate on a low-res model and render with a high res one. I can update my reference files, and they'll update all 20 scenes. My blendshapes work. My wraps work.

Maya really is an amazing program.

One other issue, that funnily enough I fixed in a old file, but am dealing with it again, is that I have a cycle error on one joint.

Another issue has to do with the low neck position David mentioned. When I went to put a new attribute on the neck controller, it wiped out my other attributes, like neck curl and "classic" flamingo pose, not to mention IK/FK switching. My work around is to have a separate file with a low neck position and use that only on the scenes that require it.

Again, I'm sure there's an easy fix or even something that demands more explanation, but I'm just going for the quick fix and this will work.