Running the <project>.restore script recreates a project with the source files and project settings that existed when the .restore file was created. However, if the project contains a System Generator source, the .restore script does not add this source back into the newly created project.
This problem has been fixed in the latest 10.1 Service Pack available at:
http://www.xilinx.com/support/download/index.htm
The first service pack containing the fix is 10.1 Service Pack 1.