How do you Update WFP?

How do you update WFP when you manually replace a .DLL or .EXE in the Windows directory? Say you have a program that needs a specific .DLL that alreay exists in your Windows directory. You replace it and everything works fine for a few minutes and then the system replaces the .DLL file. Then the software no longer works because WPF puts the old one back. How do you tell WFP you want to keep this new .DLL? Replies to aaronhill@netscape.net – Thanks