A report for the council's Employment and Skills Select Committee suggested that future versions of such a programme may suffer because organisations would not want to be exposed to similar risk Committee chair Barry Kushner said the meeting was taking place in "the context of what happened to SENW which closed last December and was a great loss to the city".
Following the meeting in Liverpool town hall, Val Jones, the former chief executive of SENW, said they had specialised in helping people from "disadvantaged areas" and their closure had left them without support.
Launched in January 2012, the project, run by SENW together with 17 supporting organisations, received a total of Au3.
Under the terms of European grant funding, SENW is required to show how all public money it has received for the BEiC project has been spent.
Failure by the SENW to do so has forced the DCLG to take action to recover the money, by issuing a demand notice.
Chief executive Val Jones has told ECHO Business that the future of SENW itself and jobs within 17 partner organisations, were now under threat.
However, in a statement the DCLG accused SENW of having "serious irregularities" in its accounts.