.htaccess in /main.domain.it path is as wp write in network configuration ( with RewriteBase / )
.htaccess in /www is untouched (but if is as wp write in network configuration, it is the same)
Do you have 2 WP installs or just one?
If it's 2, then which one are you domain mapping in?
If it's only 1 then you should only have one .htaccess.