if you haven't deleted them yet...
Make a new folder (on your desktop or somewhere else where you can find it easily) give it a name like: "Crossfire Backup Saves"
Then go to your documents folder, open the my games folder, open the freelancer folder, open the Accts folder, open the single player folder...
and you'll see all of your current save files. (they'll have random number/letter names "Save3c85.fl" etc...)
copy these to your backup folder...
Then when you've reinstalled just copy them back to the original location: Documents\My Games\Freelancer\Accts\SinglePlayer
As long as you're running the same version of Crossfire and not some different mod, you'll be able to use them all without problems.
Also...if you're playing MP you should use the "Start Menu, Microsoft Games, Freelancer, Examine my account id"
to save your mp id number so you can keep all of your mp characters after the reinstall.
If you don't have (or don't care about) your mp accounts...you can skip this part since it's not necessary to simply make backups of your saved games.
hope this helps.
-Z