settings written to the wrong htaccess

I have my wp installed in a subdirectory and the.htaccess file is located in the root dir, however better wp security kept creating a new htaccess in the subdir instead of writing to the one in the root dir which in turn messed up my entire site. Is there anyway you can add option to change the htaccess file location? Right now i work around this problem by copying the settings to the root htaccess and deleting the htaccess in the subdir, however everytime i update better wp then it is creating a new htacess again. Thanks

https://www.ads-software.com/extend/plugins/better-wp-security/