If your goal is to take your used, unchipped Xbox and turn it into a softmodded Xbox, your plan will not work, because a softmodded Xbox needs to be able to unlock the hard drive using its own EEPROM as an effective cipher. Each Xbox has a unique EEPROM fingerprint, so if you use (for example) your chipped Xbox to lock a hard drive, it will requite that specific Xbox to unlock it in the future.
I was rather wary of hotswapping at first, but have had no trouble with it; just be sure to read the 'Art of Hotswapping' thread linked in the top post of this one.
If you really don't like the prospect of hotswapping, and have an exploitable game (e. g. Splinter Cell or 007), you have use a savegame exploit to briefly mod the Xbox long enough to grab the EEPROM dump from the unmodded box, and put that on the xboxhdm CD, and you should no longer need to hotswap. See the xboxhdm thread for details.