Do you mean you're running Unbound as a DNS server for your domain(s) or do you mean the upgrade on Let's Encrypts side with the Unbound resolver library?
Because if I look at the linked error above, I think it's not applicable to the Unbound resolver upgrade used by Let's Encrypt.
However, in Unbound 1.18.0 there has been a fix with regard to some non-conforming DNS servers. See the following thread for more information: