The childcare charity was forced this month to take back a £7,500 donation to the Labour Party after a Charity Commission investigation. Charities are forbidden from donating to political parties.
Futurebuilders, the government fund that helps third sector bodies to deliver public services, announced the £2m funding for Catz Club in a press release dated 26 May 2005.
According to Clark's letter to Jonathan Lewis, chief executive of Futurebuilders, the original version of the release was still on the site last month and referred to the loan and the grant. But the paragraph about Catz Club is missing from the current version.
The letter says the list of Futurebuilders investees has been similarly amended. It asks whether the two documents were edited and, if so, why and at whose behest. It also asks about the current state of the investment.
Lewis was unavailable for comment. A spokeswoman for Futurebuilders, which is run by the Adventure Capital Fund, said references to Catz Club had been removed because "it is no longer one of our current investments".
She said the two parties had "agreed to terminate their business relationship on confidential terms satisfactory to both parties".
It emerged last week that the commission had been investigating financial controls and overdue accounts at Catz Club for the past year (17 September, page 1). Its most recently submitted accounts, for the year ending September 2006, showed £850,000 income, £4.25m expenditure and £3.5m debts.
Management of Futurebuilders transferred to the Adventure Capital Fund in April. Richard Gutch, who was chief executive of the fund when the investment to Catz Club was approved, declined to comment.
Clark told Third Sector that it seemed that someone at Futurebuilders had "doctored a historical press release".