ITunes Connect Review of an app with an incompatible API
Just in case any other person should look for a solution to a similar problem: made through Apple's reviewing process through the setup of a /2.0 subdomain for the backend. 

Every old user is still pointing to the old url and, whenever the switch is ready, we will make the old uri point to the new backend (so that we will have two simultaneous groups of URIs address the same backend).

All the old applications will still point to the old URI and get the "Invite to upgrade" message. When upgraded, all the applications will point to the /2.0 subdomain.

From a web browser people will still be able to use the old URL and get served by the new backend.