Thanks to some great comments and a specific one from James I have now replaced notepade.exe with the vastly superior notepad2.exe and prevented Windows File Protection from replacing the new notepad.
Here are the steps (warning, process with care, no warranties etc):
1) Rename Notepad2.exe to Notepad.exe
2) go to %windir%\system32
3) Rename Notepad.exe to NotepadX.exe
4) go to %windir%\system32\Restore
5) Turn off hide invisible files in Tools->Folder Options->View
6) Select filelist.xml and right click->Properties and uncheck Read-only
7) Edit the file
9) copy the newly renamed notepad2.exe (now named notepad.exe) to %windir%\system32
note: it turns out that for some folks, this doesn't work. It did not work for me on my tablet pc. Thanks to Shakeel Mahate here is method #2.
- Tools->Folder Options->View uncheck Hide protected operating system files.
- rename Notepad2.exe notepad.exe
- copy notepad.exe %windir%/system32\dllcache
- copy notepad.exe %windir%/system32
- A dialog will popup hit cancel
- Recheck Hide protected operating system files in the Folder Options dialog box
The dllcache contains copies of the windows protected files. The dllcache isnt itself protected.