If you find yourself in this unfortunate situation and are running a new enough operating system, you can restore the \steamapps\common\skyrim folder and any files contained therein to their previous versions through system protection options available in Windows 7.
1. Open explorer and browse to \steamapps\common
2. Right-click on \skyrim and select "Properties."
3. Select the "Previous Versions" tab.
In the "Folder versions" pane, you should see various versions of the folder with dates. These versions are taken from points of time whenever a restore point was created. If none are visible, you likely don't have any restore points available or you don't have system protection configured to protect the drive Skyrim is installed on. Once you select a version of the folder, you will then be able to copy over or restore individual files or the entire folder.
File deletion by Steam is the root of this problem, so it probably doesn't make sense to complain about it here (and doing so will likely result in a locked thread).
