Hi. I wish I knew exactly how it did so I could fix it or better yet report it intelligently. But no, I have no idea why it stopped recognizing my HDHomeRun in the sources or input (?) setup page. The device was still there in the admin page but it didn't show in the mythtv setup page. Trying to add the tuners back in did nothing. In fact, I could not add any of the available tuners from the drop down list; after pressing "finish" the screen was still blank with no tuners added.
On the plus side, and after cooling down a bit (sorry), reloading MCE and restoring a backup from last week fixed everything including accounts, settings, etc. It did not restore mythtv's channel lists but, fortunately, I had an open browser on another machine with the correct page loaded (http.://mcebox/mythweb/settings/channels) and simply hit the save button and all my channels were back. Good thing because that took hours to match to the listings. Overall, restoring saved me and I can live with how it all went.
Back to subject, System Recovery did not work for me. I'm not sure what a "UUID" is but, do I need to update that as well with some unique number for my installation? Perhaps that's why recovery didn't work.
Oops, just noticed I'm in the "developer" area.