If you're using ProTools, you should have your sessions (including the audio, etc.) on an external harddrive. You should only be running the software off the C drive. It's recommended. If you have the session files on an external harddrive, this will prevent them from ever being erased. Having the sessions on your C drive will eventually (over time) cause wear to the C drive, because of the amount of information required for the writing and re-writing of sound files.
You can find a good harddrive for about $100 or so.
If you have a D drive, move the sessions over there, and then uninstall the original program version before you install the new one.
I'm getting ready to do this, myself. I don't believe uninstalling ProTools will delete the folder where you have your sessions, but it's better not to take the chance.