mlemonds
macrumors 65816
If you swap your phone at an Apple store, then yes the original box will show a different serial number, but Apple provide you with all of the exchange paperwork which will give you a full record to show a prospective buyer.
I know this from having had to previously replace my 3GS because of light bleed around a poorly sealed screen.
they also give you a sticker to put on your box with the new s/n (iPhone 4s replacement)