I haven’t tested it, but what about:
add_rewrite_rule('^company/(.+)/replies/(.*)?$','index.php?pagename=replies&reply_id=$matches[2]','top');
I haven’t tested it, but what about:
add_rewrite_rule('^company/(.+)/replies/(.*)?$','index.php?pagename=replies&reply_id=$matches[2]','top');