BPS has a lock and unlock root .htaccess file buttons on the BPS Edit/Upload/Download Tab page. If you would like to let another plugin write to your .htaccess file and it is locked you would need to unlock it to allow the other plugin to write its htaccess code to the root .htaccess file.
There was a previous issue with the BPS AutoLock and file permissions checks during upgrade auto-updating that was fixed in BPS .48.9. What was occurring is that the root .htaccess file permission was being cached so the check whether to automatically lock the root .htaccess file again after the auto-update completed was failing. So now that it is working correctly you would need to choose Turn AutoLock On or Turn AutoLock Off on the BPS Edit/Upload/Download page. Most hosts allow you to lock your root .htaccess file with 404 Read-Only permissions, but a few do not. If you lock your root .htaccess file and your website crashes you will need to FTP to your website and change the permissions of the root .htaccess file from 404 to 644 file permisssions.