Well, I'm not positive of the rules on the newly-set up short course (measured second mile, that is), but I'm pretty sure it'll be run like the miles on the long course. That is, if you qualify in both (or all three) measured miles -- you can choose which one you want to select for your back up run the next morning. So - it could be the faster second mile if you wanted it to, even though you also did well enough in the third mile. There's one drawback, though -- maybe. And that's the fact that if you decide you'll use the speed from the second mile when you back up -- you've got to get your record speed in the second mile.
That is, the two runs (qualifier and return) must qualify in the same relative measured mile (even if your return is on the long course -- you'd STILL have to get your record speed in the second mile.
I think.