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If you have used the Web Update function for Altium Designer, it stores a backup copy of each update in "...\Documents and Settings\All Users\Application Data\AltiumDesigner6\Updates". You can burn them to CD's or a DVD and run them to do manual updates after you reinstall.
If you have a legal copy of Altium Designer, you can get password access to https://www.altium.com/Community/Support/Downloads/ . From there you can download all of the updates available for DXP2004 or Altium Designer 6. You just need to contact the Altium sales office where you got your copy of Altium Designer.