Ok, im im returning my iPhone to apple, and they are sending me a box to send the phone back. My phone is at 2.1, and unlocked. Well apple sent me an Email saying

WARNING: Apple has discovered that some of the unauthorized unlocking programs available on the Internet may cause irreparable damage to the iPhone's software. As part of the service process, Apple will update the software on your iPhone to the latest version. IF YOU HAVE MODIFIED YOUR IPHONE'S SOFTWARE, YOUR IPHONE MAY BECOME PERMANENTLY INOPERABLE WHEN APPLE UPDATES THE SOFTWARE. Making unauthorized modifications to the software on your iPhone violates the iPhone software license agreement, and the inability to use your iPhone due to unauthorized software modifications is not covered under your iPhone's warranty.
So if i Use Bootnueter and turn everything off, and do a restore, will what they said happen to my iPhone? Is there anything else i should do? Please help as the box is coming in a few days. Thanks