The files for his steam games should be saved on the cloud so those should be okay. I have used the refresh feature and after I put steam back on my machine all of my game data was re-downloaded.
As far as the minecraft file in the future you may consider saving that file to dropbox or some other cloud based system that will automatically back up the file every time it is changed.
I am not sure if this will work after you have done a refresh but it is worth a try.
You could try and roll the computer back to an earlier date to recover the file but this will only work if you have actually created some restore points. Here are the steps.
Open up Control Panel. (windows key + X)
Enter Recovery in the Control Panel search box, and then tap or click Recovery.
Tap or click Open System Restore, and then follow the instructions.
You will need to pick a date that is before the system refresh.
One other option would be to see if they are in the windows.old folder.
Go to the Computer folder.
Double-tap or double-click the drive that Windows is installed on (typically, the C: drive).
Double-tap or double-click the Windows.old folder.
Double-tap or double-click the Users folder.
Double-tap or double-click your user name.
Open the folders that contain the files you want to retrieve.
Copy and paste the files that you want from each folder to a folder currently in use.
Repeat steps for each user account on your PC.