The danger is that you may end up with an inconsistent machine that may not be able to boot up.
The Windows directory is only one part of the OS. A few directories under the Windows directory and more importantly the registry is backed up as part of the system state and would not be restored when you restore the Windows directory. If you are restoring the Windows directory from a backup taken a few days ago and there are changes made to these directories and/or the registry, then the two portions of the OS would not tally.
