Affa should not be writing anything to (or deleting anything from) /home/e-smith/ssl.crt on the backup server, so:
- Did you install affa as described in the SME Server wiki, or did you install the newer, more generic Centos-based affa from sourceforge?
- If you installed the sourceforge version of Affa, did you specify that you are backing up a SME server?
- Have you done something else on your affa server (such as "affa --rise", or any template or package customizations) that would affect files and folders outside of your affa backup folder?