new games often give u the option to save the content if you uninstall it but older ones often dont.
to be safe i'd just save your save file to desktop and replace it with the new one thats created once you've reinstalled correctly (added the same patches)
thing is though you shouldn't have to reinstall i dont think. just start using the new disk.
or you could save yourself �5 and download the no-cd fix from www.gamecopyworld.com , install the fix and your comp wont go looking for the cd and you can then play without it.