I assume you mean the .htaccess file that throws an error on delete or edit ?. So you can't delete the directory ?. If you comment out the exception routine (ie: ## ($file =~ m,^\.,) and return ($file, "no leading '.' in file names.");), you can remove and edit the htaccess file from within fileman. In the meantime, any semblence to security is gone but for admin stuff - hey, you are admin....:)
good luck