Right, I've done this now but I reflashed the NAND as well and am now back to a clean install. At least my /data is intact.
I flashed the NAND, reinstalled the latest hdd image and then used the pdaxii13-custom.tgz to upgrade. I did all of this from the installer menu. It's no big deal, I'll just set it back up again and reinstall my extra apps but please could someone confirm that to upgrade in future all I need to do is install the hdd image and use the latest pdaxii13-custom.tgz file and that this will upgrade my kernel and installation to the latest version.
Also, I have noticed that on the Info tab of the config tool it now says pdaXii13 build 5.4.8 "Alice". Should this not be Sally or Akita on an SL-C3200.
Thanks for the help.
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updater.sh is the installer program
tools.tar contains some tools required by the installer and also contains the updated kernels (the kernels don't change very often so there is no need to redownload this file each time)
initrd.bin contains the rootfs and other skeleton filesystem. by flashing this file, your flash will be wiped and overrridden with the content of the initrd.bin
hdimage-full.tgz contains the extended rootfs for the MicroDrive capable Zaurii and by installing it, the roofts and all its contents are also overridden, ie the contents of the first MD partition is overrriden with the contents of the hdimage file. The third partition (mounted as /data) is not touched.
for most upgrades, all you need is updater.sh, tools.tar and pdaXii13-custom.tgz which just updates various files for you but won't require you to replace your rootfs which the initrd.bin and hdimage-full.tgz requires
when doing the upgrade using the pdaXii13-custom.tgz, some of the packages are not updated and requires you to manual upgrade those packages as described in the release notes.