Uhm, don't do an inplace upgrade anyway, they suck. If you have /home on another drive, there's no "backup" or "restore" stage.
Regardless, it's easy to not lose your setup, run the latest OS AND not do in-place upgrades.
Just put /home on a separate partition and you're done. Use dpkg to make a list and restore a list of applications (same with repos). A few files to backup and a few minutes to wait for the apps to redownload. Completely clean system. Same apps. All the while /home was untouched.
#apt-get -f missing
fixes many of these post-upgrade problems. YMMV!