Many things have changed with W3TC so maybe you are not actually using or have any W3TC .htaccess code. To make the error check go away do these steps.
1. Copy this text: # W3TC Error Check to this BPS Custom Code text box:
2. Click the Save Root Custom Code button.
3. Go to the Security Modes page, click the Create secure.htaccess File AutoMagic button and activate Root folder BulletProof Mode again.
4. Refresh your Browser and the Error Check should go away.