Your hard drive won't change. You will keep your programming. The settings, however, are a different story. If your using Win XP, you will also most likely have to re-register with Microsoft due to the changes.
I would also bet on having to re-install several of your currently installed programs as well. Again, this are major changes your making on the hardware side and it does affect how the Operating System works.
Win XP, when it boots up, has "X" amount of points that it looks at while booting. If a certain number of these points have changed, then it asks to re-validate. This is one way that MS insures that 1 copy gets on 1 computer.
Many of your programs will also need to be re-installed (simply install them again). Pretty much because you've made changes to how your system works and runs, many of the software drivers will be different and how they interact with the hardware will be different.
My suggestion would be to back up your files to DVD or tape. Go ahead and do a fresh install of Win XP (Reformat and the works) and re-install your programming as needed. This will help your system run that much faster, it won't be bogged down with all the little bits and pieces of software that's been un-installed and debris left behind.
It's a pain, but well worth the trouble.