Your best option in that case is to run the CHKDSK in offline mode from a Repair Environment boot.
Reboot the computer, and tap the F8 key until you get the advanced boot menu up - one option should be 'Repair your computer'. Pick that one.
Log into your normal account.
You'll get a set of options - pick the Command Prompt one.
At the command prompt, type DIR C:\
- if we're lucky this will bring up a listing of your normal C: drive contents, including the Program Files folder(s) and the Windows folder.
If not, try D:\ or E:\ (etc. until you get the right letter)
then type the following command
CHKDSK <drive>: /R
and wait for it to complete - it could take a few hours, depending on the size of the drive.
See if that works.