In Apache 2.4, access control has changed. v2.2 syntax will still be supported for a while, so code added to .htaccess by Defender works in 2.4.
But when we want to make use of v2.4 features, problems can arise when adding new directives to the old. See: https://httpd.apache.org/docs/2.4/upgrading.html
I recommend that the code which updates .htaccess should check the version of the web server, and use the latest directives available for that release.