There is a sub-assy that is using flexibility to suppress components. All the red X's are in this sub-assy. Suppressing that assembly, allowed renaming everything and save a copy to work. (Thanks to a suggestion by Neal Hanratty.)
Essentially the full sub-assy has a straight and a bent version of a couple of components. Instead of using a family table to select which to show in the upper assembly they are using flexibility.
Not sure why this should cause a problem. I can bring up the sub-assy and save a copy on it with no issues, but then it doesn't have flexibility at that point.