I heard that you actually can take the iphone purchased online and return it at the store. Although the return policy online does state that iphone purchased online through the Apple.com can't be returned at the retail store.
As for the eligibility reset, it can take 24 hours up to 72 hours for it to reset.
I had this issue where I returned the phone and my eligibility was not reset. AT&T couldn't reverse it because I purchased it at the Apple store. Apple store tells me that it's AT&T issue. Anyways if you purchased through Apple, it will be an Apple issue to fix.
However because of the AT&T Next that I used. It was an issue with the financial creditor (helafax), because on Apple system it does show that my phone was returned. Also on AT&T side as well. So it got stuck in the creditor state. So the rep who bridges Apple and AT&T at my apple store is the one who can reverse the upgrade.