Currently the official website shows just one option, if I'm right it's the very straightforward etc., while the hilly one has been removed from the webpage. You can still find the hilly option in the zipped download of the gpx tracks and of the routesheet, though.
Something more definite has happened with the first leg, Loughton - St Ives, where there was a route suggested for the morning and another for the afternoon: now there's just one route, I think the afternoon won.
On the way back, the "to Cambridge or not to Cambridge" question has currently the same status as Brampton-Moffat: no visibility on the webpage, but (still?) present in the zipped downloads.