Simply deinstall and reinstall. The configuration files and other information in the .virtualbox directory are not purged that way.
# dpkg -r virtualbox_1.6.2-31466_Debian_etch_i386 # dpkg -i virtualbox_1.6.2-31466_Debian_etch_i386
The VM virtual drives are just big flat files in /home/username/.virtualbox. Back them up along with the rest of your data files.