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.exe2) go to %windir%\system323) Rename Notepad.exe to NotepadX.exe4) go to %windir%\system32\Restore5) Turn off hide invisible files in Tools->Folder Options->View6) Select filelist.xml and right click->Properties and uncheck Read-only7) Edit the file8) Add:
<Exclude> <REC>%windir%\system.ini</REC> <REC>%windir%\tasks\desktop.ini</REC> <REC>%windir%\win.ini</REC> <REC>*:\AUTOEXEC.BAT</REC> <REC>*:\CONFIG.MSI</REC> <REC>*:\CONFIG.SYS</REC></Exclude>
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.
The dllcache contains copies of the windows protected files. The dllcache isnt itself protected.