Yes, I think that's how I understand it as well to be honest. Routes require DfT permission to be removed and if the DfT has not be consulted the change is considered "illegal" and the old route is still legally valid, I think. Presumably this covers the fares check as well as mapped routes. I'm afraid I don't really know what a "Protected Route" is.
NRE offers journeys Southport to Manchester and return via Moorfields and Lime St and via Hunts Cross on the same Open return ticket as the direct route.