Food Dudes, created by Bangor University after 25 years of research, featured superheroes who gained special powers by eating fruit and veg.
It has been credited with helping more than 700,000 schoolchildren across the UK, Europe and the United States.
The liquidation of Food Dudes Health Limited is expected to be concluded in the next three months.
The Food Dudes scheme - which included DVDs featuring the superheroes - was developed following research by Bangor University psychologists and was rolled out to schools in the early 2000s.
In Ireland, it was introduced in all primary schools.
In 2012, the running of the project was transferred to Food Dudes Health Limited, although its board consisted of three Bangor University academics.
That company went into liquidation in 2015, and the liquidation process is nearly complete.
Among the list of creditors are public health bodies and councils in England, which are owed more than £800,000, and Bangor University itself, which is owed more than £200,000.
Liquidator Ian Brown, of Liverpool-based Parkin S Booth & Co, said: "On 17 March 2016, the company's intellectual property rights were sold to Bangor University for the sum of £20,000.
"Part of the sale included the rights to the name 'Food Dudes Health' and hence a change of name to Grub Men Ltd was registered on 3 May 2016."
Bangor University has been asked to comment.
A company which ran a healthy eating project for children is in liquidation with estimated debts of £1.2m.