I'll start by saying I don't know for sure. Some thoughts to share though:
Anything anyone here tells you will be irrelevant if you do the swap and Apple.com refuses the return. Same for if someone in the retail store tells you it's fine; unless it's in writing I wouldn't trust it. It'd be my luck to get the one employee who doesn't know Jack Sht and tells me wrong info.
Since you're within your 14 days but nearing the end, I'd suggest you decouple the transactions. Buy a new one at the Apple retail store. Return the existing one. No possible headaches with different serial numbers and you've reset the 14 day clock.