Hi,
If you mean System Restore, I don't think it will restore the deleted folders...
The deleted folders would probably be in the Recycle Bin, but if you are concerned about this, don't delete them...
Just Rename them with something simple like an "A" at the beginning of them name...
Like A0002, A0003, A0004, as an example....
As far as windows is concerned it will have the same effect as deleting them...