put the cert back, in System Manager under Services/sercutity/certificates/Authority click on the CA Structure & CRLs, Download the PEM file. You should end up with "SystemManagerCA.cacert.pem" in your downloads folder, web browse the CM, under Server Maintenance go to Miscellaneous/Download Files, select check box for files to download from the machine I'm using and click on choose file, select the .pem file and select download. When it finishes go to Security/Trusted Certificates, click add and enter "SystemManagerCA.cacert.pem" in the box, give it a name (SMGRCERT is popular), tick all trusted repositories, click add.
Try the sync again.