M program doesnt do anything to the system files. 90% of the repairs are all in the registry, so normally just restoring the registry to before the repairs is all that is needed.
The pre scan just looks for missing files and signatures, the files it knows to look for it pulls from "HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Component Based Servicing\Packages"
That is the list of files that are suppose to be in the packages folder. The pre scan loops through that registry key and if there is an entry in there but the file isnt in the folder then it will show as missing. Then after it looks for any missing it then calls the windows api to report if the files have a good signature or not, that is just a true/false return.
Cat files have their digital signature on them, the point of a cat file is to hold the hash values of any files types that cant hold a digital cert, in this case the .mum files. They are just text files in xml format you can open in notepad. So when the programs asks windows if the hash is good for that mum file windows goes and checks the cat database, if the cat file isnt there or if it is and the mum files was changed somehow then it will report back as bad.
Now if you installed any updates after the registry backup then those updates could have simply removed some older updates and thus the files would be gone and it would also be removed from the registry path I gave you. But if you restored the registry after that happened then those would show up in there again and thus the program shows missing files.
If that is what happened then I would just ignore the pre-scan. But remember the program doesn't remove or modify any of those files or any system files. The only files removed are temp files and the cache from windows updates when you run the windows updates repair. Otherwise everything is done in the registry
Shane
Shane