If the short name changes, you will get an alert that says:
"Some of the items you selected cannot be automatically restored. Click Save to choose where you want to restore these files. If you restore files that belong in a specific location, such as application preferences or user data, drag these from the restore folder to their proper locations."
This happens because Backup remembers the directory path of the files it saves, and your user's short name is part of that directory path. If you do change short names, you can copy the files to your hard disk and then drag them to their proper location.