The following commands helped us to re-create the self-signed certificates.

http://www.zimbra.com/forums/administrators/44241-solved-solved-zimbra-6-0-1-stop-working-if-ssl-certificate-expired.html

Single-Node Self-Signed Certificate
1. Begin by generating a new Certificate Authority (CA).
zmcertmgr createca -new
2. Then generate a certificate signed by the CA that expires in 365 days.
zmcertmgr createcrt -new -days 365
3. Next deploy the certificate.
zmcertmgr deploycrt self
4. Next deploy the CA.
zmcertmgr deployca
5. To finish, verify the certificate was deployed to all the services.
zmcertmgr viewdeployedcrt

su – zimbra
zmcontrol stop
zmcontrol start