You cant upgrade from XP64 to vista, only a clean install!
http://www.microsoft.com/windowsvista/getready/upgradeinfo.mspx
And what did the XP installer do when upgrading from an earlier version? Delete the current installation and in some instances compress those files for later reversion. The Vista installer especially a 64bit version will obviously "delete" the current in favor of it's own installation. It may even now detect and remove a 64bit Linux distro?
When you upgrade it does not delete the current install, it overwrites files on it and the only time it will compress the overwrote files is if you ask it to.
There is no upgrade from XP64! to Vista
When installing XP to ((replace 98)) on a 98/Fedora drive the installer didn't overwrite but deleted "all" 98 files.
The upgrade from XP64 to Vista would obviously be Vista's deletion of the older version.
Finally
You finally figured that out?Even when going to reinstall XP the current installation is deleted during the process. But of course you? already know that. (hhhmmm... I wonder)
(Your) the one that said to start with, you could upgrade from XP64 to vista. You can not! Only a clean install!!