Yes I keep most of my programs on a separate partition from windows however a reinstall of the is required after a fresh install of windows if the program has registry entries in windows. The data save on the separate partition is not affected so often tweaks to the program remain the same, sometimes you get the option just to repair.
Stand alone programs are not affected.
For this reason I image the drives regularly so may only lose a weeks worth of info at most and all important info is backed up at time of making.
As for the codes they shouldn't be a problem as there are no hardware changes and they are being installed to the same computer.