Use the file scan to get Defender to offer an update to the root-level .htaccess file. Now break the environment "accidentally" and do another file scan. Not knowing that it has already updated .htaccess, it adds a new block at the bottom of the file.
The code should scan .htaccess for its own markers:
## WP Defender ...
## WP Defender - End ##
Delete that code, and then add the new block to the bottom.
This is especially important because that .htaccess code changes between releases. We could assume that a duplication of the code would have no ill effect, but if an update includes a correction, if the old block isn't removed it will still have the bad code, and at that point there could be some undesirable behaviour.