Will doing a re-install of windows XP remove my program files or make them not work?Reinstalling Windows XP will format your Harddrive and will only RELOAD Operating System files. So yes, you will lose your programs. They will not work because they won't be there.

However, if you want to keep your files (pictures, documents, and such) will MUST save them to EXTERNAL media before you begin the installation. External Media may include a USB thumb (flash) drive, CD, DVD, Floppy disk, external harddrive....you get the idea...After installation is complete, you simply reload them.

As far as your programs are CONCERNED, you would have to reinstall them after the Windows XP installation is complete.There's another option actually...
Repair Install of XP

Done properly your data and apps will remain intact.
Done improperly your apps and data will be gone but you will have a fresh install of Windows.

I suggest reading it thru a few times before starting and printing out a reference copy...Yes, the repair install works as advertised.
And there is an option to reinstall to a DIFFERENT folder windows001 as an example