A previous consultation on the preferred route had included proposals for a new ‘core’ line running from Wimbledon via Tooting Broadway through central London to Angel, with a branch line serving Hackney Central and a main line continuing onwards towards Hertfordshire.
A further branch line to New Southgate in the London Borough of Haringey via Turnpike Lane was also previously proposed.
According to the latest consultation documents, the Hackney link has been dropped from the first phase of the project but could form a "potential future eastern branch".
The connection at Tooting Broadway in the London Borough of Wandsworth has also been dropped in favour of a station at Balham.
There are also proposed changes to the New Southgate branch line with a new option of running the line via Wood Green rather than Turnpike Lane and Alexandra Palace.
Further details have also been published on possible connections in the south west of the capital using existing rail lines.
There would be four regional branches serving Shepperton via Kingston; Hampton Court via Surbiton; Chessington to South via Tolworth, and Epsom via Worcester Park.
A consultation said the regional services "would serve a number of regeneration and opportunity areas in north and central London, providing sufficient capacity to support 200,000 new jobs and accelerate and enable the development of 200,000 new homes."
The consultation runs until Friday 8 January 2016.