Mr Towers wrote to Justice for Rover Workers campaigner Oliver Thomas in 2010 to say that all assets of the finance and lease loan book firm would be swallowed up following a claim from the Pensions Regulator.
Last week's announcement of a settlement with MGR Capital's liquidators Begbies Traynor freed up around £12 million, with approximately half being shared between Mr Towers and four other former Phoenix directors.
But back in May 2010, Mr Towers wrote to Mr Thomas to say: "In your letter you seem to confuse Phoenix Venture Holdings with MG Rover Capital. It's important to understand that MGRC is an entirely separate non-Phoenix company which has no connection to the Trust. It is now in a liquidation process and subject to claims which, if allowed, will wipe out its entire assets."
The Phoenix Four and former MG Rover chief executive Kevin Howe learnt last week that they were eligible for around £1 million each from the proceeds of MGR Capital nearly ten years after the car firm closed with debts of more than £1 billion.
The five had been accused of paying themselves around £42 million in pay and pensions over five years before MG Rover's collapse but the ex-directors say the figure should be reduced to £37m, following payments to the senior pension fund and other costs.
They were accused by a Department of Trade and Industry inquiry in 2009 of lining their own pockets and other management failings.
Now, in a new letter to Mr Towers and the other ex-directors, Mr Thomas says: "Contrary to the assets being wiped out, it is reported this week that the Phoenix directors are to receive another multi-million payout in the near future. I write to gain your feedback on...if this money can be made available to the ex-workers in light of the shortcomings to the Employee Trust Fund."
It is understood that the liquidation of MGR Capital is still under way, and the five ex-Phoenix directors should receive their £1 million payouts – before capital gains tax – in the New Year.
The Phoenix Four – John Towers, Nick Stephenson, Peter Beale and John Edwards – agreed to being banned as directors for a combined 19 years, while promises of payouts to 6,500 workers from the Trust Fund died following a claim from banking giant HBOS.
Mr Towers could not be contacted for comment.
But a source said: "John Towers and the other directors had felt that the claim by the Pensions Regulator covered the whole of the assets of MGR Capital – they had pretty much written it off as coming to nothing."