Of course u should not use it on working programs. Its meant to be used for programs which use Windows Installer and get stuck halfway and exit leaving all config files in temp dirs. If u re run setup for such progs, it may fail and here's where this thing helps you. run it and you will see all the programs which have used Windows Installer [note installshield also uses windows installer] and have config infos stored on disk. remove the info of the problem app which wont get installed. After removal re run the apps setup and it should work.
If u use it on a non-problem app, u'll end up deleting all record of that program being installed and u'll never be able to uninstall it. Hence the warning.