LOL, yes, if you uninstall and then re-install, your save games will be OK. Just to be safe, I recommend that you back-up the savegame directory (just zip it or something).
I also recommend that you do the full install if you got the room on your HD. It will make the game faster and more realiable 'cause you'll never access the CD except on the opening screen.
Good luck, keep us posted.
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