Hi Doug -
It sounds like maybe your separate track might not have actually been an independent track, but some kind of duplicate/alias of the original track..?
I'm a Logic user not a Cubase user, but Logic & Cubase are similar in many ways, and I know that in Logic it's possible to have Regions that are aliases of other Regions -- aliases are not independent Regions, so if one is edited they're all changed -- is it possible in Cubase that something like that may have happened here..?
Another possibility that occurs to me is that maybe you somehow rendered the VariAudio edits, changing the original audifoile (which would then be affected on all tracks)..? That seems less likely, but perhaps not impossible..
I've attached one of our Cubase courses to this thread -- maybe a true Cubase guru will be able to provide a more definitive answer..