Just do not care. Just do not use the output of the mux and do not use the pins in question. The internal routing does not matter when you do not use the resulting signals.
I have a project where almost all pins and most of the analog resources are used. Now I am programming this on another board. For this, I want to make sure pins do not have any connection to the internal circuitry.
Yes, I have resorted the same trick. I am leaving mux outputs to no-connect. Thanks.