Try locking your Root htaccess file to prevent other plugins and themes from “flushing” (doing a wp rewrite flush) or writing to your Root htaccess file.
1. Go to the BPS Pro > B-Core > htaccess File Editor tab page
2. Click the Lock htaccess File and Turn On AutoLock buttons.
If you cannot lock your Root htaccess file due to web host restrictions/limitation or for some other reason then another option that you can use to solve this recurring problem is to exclude the Root htaccess file from being checked by AutoRestore|Quarantine.
1. Go to AutoRestore > Add|Exclude Other Folders & Files > Exclude Folders & Files.
2. Select Exclude an Individual File option.
3. Enter the path to your Root htaccess file. Example: /xxxxx/public_html/xxxxx/.htaccess
4. Click the Exclude button.