Lighter wrote: It may not be surprising that the patricidal stanzas seem to have been added (probably postbellum) in West Virginia, a politically divided "Border State" made up of Virginia counties that refused to secede.

While I think your hypothesis likely, I have to add a nitpicky point: Virginia was a politically divided border state, but what became West Virginia, while it had some secessionists, was far less divided than the state as a whole: The large majority there seems to have opposed secession.

This was pretty typical: the Appalachian regions of the southern states (Virginia, North Carolina, Tennessee, Georgia) were all basically anti-secession. Abraham Lincoln spent the first two years of the war trying to induce some general -- any general -- to invade East Tennessee and bring it back into the Union. The mountain people's desire to stay in the Union isn't really surprising; the Appalachian regions had no plantations, and few slaves, so they had no reason to want a change.

In the Interesting But Unrelated Footnotes department, there is some reason to think that Thomas C. Dula ("Tom Dooley") deserted from his North Carolina regiment during Sherman's North Carolina campaign. Dula was from the Appalachian region of western North Carolina -- the reason he fled to Tennessee after the murder of Laura Foster is that it was close. So did Dula desert (if he did) because the Confederate cause was hopeless and there was no point in getting killed, or because he had little social conscience -- or because he was from a part of North Carolina that, on its own, probably wouldn't have seceeded anyway?