You normally get the Windows.000 folder when you copy your windows setup files to your hard disk and run setup from there or when you reinstall Windows, since C:\WINDOWS is the default install path.
Assuming you did agree to install Windows to C:\WINDOWS.000 then the file is the support information for Macromdia Flash Player, which you have either installed independantly or as part of the Flash program.
If you installed Windows to C:\WINDOWS and the C:\WINDOWS.000 filepath is the result of a reinstall and is not being used, you could rid yourself of the files in there, but it sounds to me as though you are running Windows from within that directory so you'd be best off leaving it well alone.
A very simple workaround would be to navigate to your C:\WINDOWS.000\Application Data folder and select the Macromedia folder and move it and everthing in it temporarily to C:
Run scandisk and then move the folder back to where it belongs after scandisk has completed. Remember to do this or all hell breaks loose next time you try to use Flash or your other Macromedia programs.
Hope this helps.
Give my best to Belgarion and CeNedra