Better WP htaccess and config

I got hacked and not too much damage. Nice hacker, I suppose. It only cost me about 12 hours to fix it.

Immediately installed Better WP and went through settings. Initially, I decided to not enable the htaccess and wp-config editing by Better WP.

Question: Will the late enabling cause all the settings made to require my manual input, or will Better WP find them and make the edits after the fact?

Thanks