Ok take a look at this Forum Topic link below to get familiar with how multiple website domains – hierarchy, structure, relationship affect each other. Basically a Parent website’s htaccess file will affect all Child websites since the Parent site is higher in the folder structure: /parent/, /parent/child-1/, /parent/child-1/subfolder/, /parent/child-2/, etc.
http://forum.ait-pro.com/forums/topic/htaccess-files-for-multiple-website-domains/