Half of the surprise was that the Xubuntu upgrade replaced my previous GRUB setup. The Master Boot Record was previously linked to my Debian partition. After the upgrade, the MBR was linked to the Xubuntu partition. I saw the same behaviour from Xubuntu, Kubuntu and Ubuntu 11.10 before, so I was not shocked.
Changing the bootloader without the user’s permission is not acceptable, I believe. I can understand that a newly-installed operating system installs GRUB without explicit permission. But this time round, I ran an upgrade. The Xubuntu upgrade should not have replaced the existing MBR.