Tonight we learned that our new workflow to fix the corrupted editing project file was incomplete.
There was still an oddity in our cleaned project test files. Duplicate Video Sync master clips were showing up and acting like they were subject to quantum entanglement (or as Einstein called it: "spooky action at a distance"...an apt description given our seemingly-haunted project file). Essentially, what happened to one clip affected the other despite that they looked like totally separate (though duplicated) master clips.
After further troubleshooting, we had a solution: take a knife to the XML file that routes between the editing programs and simply cut out the offending duplicates before importing back into the final project file.
The essence of simplicity.
And it worked like a charm.