eCart wouldn't have wiped them since eCart doesn't have any security assist functionality. PowerCMS and Security Assist could have overwritten each other somehow. It is also possible that you had an older version of the rules installed and you have installed a newer version of one of our extensions so it is just looking in the wrong place since we changed the directory structure years back.
Anyway, to restore them you can upload webassist/security assist/helpergroupsrules.php for the latest version or WA_SecurityAssist/helpergroupsrules.php for older versions.