Umm, I might be able to direct a little bit, but you need to clarify that first post. "blink:

You have two stores running right now, one the original and the other an upgrade. Is that correct?

"Ignore configure files..." You mean the configure.php files? SO establishes and utilizes some configuration parameters in the DB. If you are running two different stores, I imagine that you also have two databases. It's only going to look at the configures of the chose DB, as set in configure.php. Am I missing something?

I have no idea what you mean by "defaulting to old file sets." SO doesn't involve templating, so I won't even guess what you're alluding to here.

From your post I gather that you might be upset. If so, I can appreciate your frustration, and am happy to help if I can. However you have to lay out exactly what's going wrong.