Hmmm, after some more digging I think I may have found the basis for what confounded me about the Net Classes transition from V6 to V7. While re-configuring my forum search for issues related to Net Classes in V7 I came across these two posts:
I just went back and skimmed the Schematic Editor Reference Manual section on Net Classes as noted in these posts and now see there was a change in how Net Classes are handled now in V7 (patterns, etc.). I didn’t go back to the reference manual after upgrading to V7 foolishly thinking “well probably not that much changed”. In all fairness, I didn’t see anything about changes to Net Class handling in the release notes…but I could have missed that too. Anyway I think answers to my questions about disappearing Net Class entries in the Setup Configuration are probably answered in the updated Schematic and PCB Editor reference manuals. I’ll have to determine what actions I might have to take to make sure my Net Class information is complete, and probably circle back to confirm my suspicion and close this thread.
Like someone a long time ago use to say: RTFM. 