Hi, Tyro.
What a mess. Usually system files in the Windows folder are protected from being deleted by users, but not all of them.
Here are some ideas:
Go back to the Microsoft store and tell them to fix it. They caused it, it was their mistake, they are responsible to fix it.
If that is not possible because they are too far away... find another Microsoft Store if possible and have them fix it.
Last resort: If it was me, I'd just back up all the files that I care about onto my SkyDrive (now OneDrive) account or a reliable thumb drive. Then do a factory re-image. Maybe back up the files and make the MS store do it. If I had purchased Office
2013 (it sounds like you have Office 2013), then I would have them reinstall that as well.
Keep the store involved because it is their fault.
At least call the MS store in San Diego and ask them what they suggest. Put them on the spot. They are the ones that screwed up and are responsible for the copying process.
Good luck!
Best wishes, Davin Mickelson