To prepare an iPod Hard Disk for reinsertion into the iPod unit after performing an IDE-access level recovery or repair you should follow several steps. First things first though–make sure you run a full diagnostic on the drive.
Perform this routine with only the iPod hard disk connected to the IDE bus in an environment provided by either a boot CD or floppy. The Ultimate Boot CD provides an excellent environment for executing hard disk diagnostics and a variety of useful tools and utilities. Along with others, I’ve found Hitachi’s Drive Fitness Test to be top notch when it comes to thoroughly testing iPod hard disks.
If your drive passes the diagnostic you should prepare it in a RAW format before placing it back into the iPod. Essentially, wiping the disk is what is necessary, and Collin over at Command-Tab first wrote of using Darik’s Boot and Nuke (DBAN) to accomplish this. I suggest reading the article by following the link for more detail.
I personally can vouch for the effectiveness of this procedure. The DBAN utility will take a long time to run in its default configuration so be prepared to entertain yourself doing something other than watching its progress. It took over 2 hours recently for me to DBAN a 20GB iPod drive.
Once this process is complete, though, it is well worth it. Simply reinstall the hard drive into the iPod, place the iPod into Disk Mode, and run the iPod Updater. This works for the simple reason that the formerly corrupt data on the drive doesn’t exist, and is no longer in conflict with the iPod and its attempt to boot malformed code.