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I've had 3 replacements over the years while running beta software and Jailbreaks. They've always noticed and asked me questions about it to check it wasn't related then proceeded with the replacement as per normal.
 
I recently checked out this thread to figure out whether the downgrade from ios 7 beta to 6.1.4 was even possible on my iphone 5, since I recieved a replacement phone and need to send the old one to apple. I reset the iphone to factory settings while it was still on ios 7 to simply delete all the content, this is where I got an error message from itunes saying that "This device is not registered under the Apple Developer program" and thus could not be activated. At this point I was thinking I was SOL (I am not registered as a developer), but figured i would try some different methods. Using Redsn0w 0.9.15b3, I was able to manually select the 6.1.4 firmware without having to go through Itunes, worked first try. I figured after so much arguing and stress over wondering if it is possible to get an iphone warrantied that is on ios 7 I would share this method. This is my first post on the site but ive frequently been on here observing. hope this helps someone in the warranty process
 
I recently checked out this thread to figure out whether the downgrade from ios 7 beta to 6.1.4 was even possible on my iphone 5, since I recieved a replacement phone and need to send the old one to apple. I reset the iphone to factory settings while it was still on ios 7 to simply delete all the content, this is where I got an error message from itunes saying that "This device is not registered under the Apple Developer program" and thus could not be activated. At this point I was thinking I was SOL (I am not registered as a developer), but figured i would try some different methods. Using Redsn0w 0.9.15b3, I was able to manually select the 6.1.4 firmware without having to go through Itunes, worked first try. I figured after so much arguing and stress over wondering if it is possible to get an iphone warrantied that is on ios 7 I would share this method. This is my first post on the site but ive frequently been on here observing. hope this helps someone in the warranty process

Glad this method worked for you, but the simplest way to go from beta software to regular version is to put your device into DFU mode and then restore. That does need iTunes, but you probably have iTunes anyway -- you need iTunes to install the beta in the first place. So DFU and restore with iTunes, no need to go hunting for redsn0w or other such software.
 
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