.htaccess should not affect default sites..
but my guess is cause stock .htaccess does have things like rewrite in it, it could error out maybe..
prob no harm in removing the .htaccess file from root folder but there is alot of other folders that use it..
removing all .htaccess files will leave your dirs open to attack and people could tech find out your db info if removed the .htaccess from say include!!
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