The Super Patch will let you patch. I've had "File Not Found" errors for several patches now.
However, you will probably need to use the Super Patch every time. If you want to get rid of it, the only solution I know of is a full reinstall (not a Factory Reset), because you've got a file somewhere that either A) shouldn't be there B) should be there but isn't or C) is there, but isn't what the Patch expected to see there. Without carefully scrutinizing your files against someone who doesn't have this error (which would take ages anyway), the only way is to reinstall.