I had the exact same problem and same symptoms. Wouldn't boot, did the refresh, which wiped installed apps from the system. I could boot to windows and log in but couldn't access my C: drive (where windows was installed) but I could access other drives no problem.
Hard drive is fine as was able to boot widows. So this felt like a user permission problem.
Indeed I was able to gain access to C: again with the following method.
1) go to desktop and open file explorer
2) right click on Computer->C: and select properties.
3) Click the Security Tab
Here's where my memory is getting a little foggy but you essentially need to add "Users" back to access list for C: drive.
I think there was a couple of steps I had to do here to enable me to continue but I can't recall exactly or reproduce this. (maybe someone can add the details...?)
4) click "Edit"
note that only Administrators and SYSTEM have access to the C drive. Now even though my logged in user was originally an Administrator, it appears the refresh process removed those permissions.
5) click Add
6) in the "Enter the object names to select" box type "users" and hit Check Names button, should replace with [your system name]\Users
again don't recall exact details but essentially checked "allow" for nearly all permissions.
7) click Apply. get some warning from Window security about changing permissions of root directory of startup disk. .... can reduce security of computer... do you want to continue? I said yes. then it went through basically the full C: drive and tried to change permissions on all files. got hung up on some system files that were in useby the SYSTEM but at this point I didn't care.
I'm interested in hearing from other what these settings should actually be!
this appears to be a problem with Microsoft's Refresh mechanism. It probably locks down the permissions to the SYSTEM only for the refresh but the developers probably forgot to restore user permissions to the C: drive.