Actually the backup should have the certificate too. According to the documentation :
Components Backed Up
The ACS System Backup feature backs up the ACS user database that is relevant to ACS. The user database backup includes all user information, such as username, password, and other authentication information, including server certificates and the certificate trust list.
If your ACS for Windows logs information to a remote ACS server, both ACS versions must have identical release, build, and patch numbers; or the logging might fail.