I may be wrong, but, I am pretty sure you may be able to extract the
firmware from the Apple ipod updater, and then just use that firmware
and install the rockbox bootloader again, without having to use the
Apple utility.
The instructions are at the same location of the installation instructions,
http://www.rockbox.org/twiki/bin/view/Main/IpodInstallationAnd if you look under section c.2, You'll notice it mentions something about
extracting the apple firmware from the iPod Update utility using
IpodWizard, at
http://www.ipodwizard.net/.
Then you should just be able to reinstall the bootloader, using the same
instructions, with instead the new extracted firmware.