AVTS 3-13-1-4 - Los Angelas - Main Audit file mismatch

Doing testing here in Los Angelas, after inserting a managers card and selecting Supervisor Functions, then put in pin number, and finally hitting exit, system begins to load election again and then gets Error Message - Main Audit file does not match Secondary Audit file. Any suggestions on what the problem is here??? Once you say OK, it then says Secondary File does not match Main File do you wish to overwrite. If you say yes, then system takes 2 hours to rebuild database, and don't know if you loose any votes???