To make things simple and to isolate possible problematic custom .htaccess code this is a good approach.
Go to Custom Code and cut (not copy) all custom .htaccess code to a Notepad or Notepad++ document and save it.
Click the Save Root Custom Code button.
Go to the Security Modes page, click the Create secure.htaccess File AutoMagic button and activate Root folder BulletProof Mode.
At this point you will have only standard BPS .htaccess code in your root .htaccess file.
Then add any custom .htaccess code in stages by only adding 1 bit/block of custom code at a time to 1 Custom Code text box, rinse and repeat the steps above and test everything. If everything is ok then add another bit/block of custom code, rinse and repeat...