Contact Department and Motor Vehicles and ask them what they will accept. If the Naturalization Certificate did exist, you can get a new one, it just may take some time as well. Contact the Dept of Homeland Security for that information.
The answers given are limited to the facts as given and presumed by the answer itself. Without seeing actual written documentation or having a conference to more fully explore the issues, this short answer has only limited application. Make sure to seek legal counsel and provide all documentation to get assistance in making informed legal choices.