How do I use rsync with an IPv6 address via SSH?

You'll want to wrap the address in brackets like so:

rsync -rtlzv -e ssh /path/to/src 'root@[fdff::ffff:ffff:ffff]':/path/to/dest

Try placing the IPv6 address in brackets, like this:

root@[2001:db8:1234:5678:feed:face:dead:beef]:/path