If your Ruby Base is in the same place as your Emerald Base, it won't appear. If it isn't... weird. I've heard of cases where even registered Bases disappear in a mix, though...
The TV programs are randomly obtained, unless they're event programs. Say, if your Ruby is about to have the Lilycove Clear-out sale, mixing with Emerald will give it the same event. HOWEVER, if you haven't beaten the Elite Four at least once, that won't work.
Those are the only reasons I could find...
