There are no differences between the root and wp-admin .htaccess files in BPS free and BPS Pro. They are exactly the same. BPS Pro B-Core functions exactly the same as BPS free htaccess Core in regards to the root and wp-admin .htaccess files. There are of course many additional things added to B-Core in BPS Pro, but the root and wp-admin .htaccess files are identical in free and Pro.
Instead of trying to figure out what has happened on this site here just send me a Super Admin login to this site so I can see what happened. I assume it is a simple mistake that can be easily corrected. Send the login information to: edward at ait-pro dot com. Thanks.