A moot point now, but instead of filing PF for two years they could have filed form 8940 to receive retro recognition as a Public Charity.
Sounds like they need some sound advice on the difference between a Public Charity and a PF.
For a PF they need to be aware of the minimum distribution requirement, self-dealing rules, serving a charitable purpose among other concerns.
Maybe a reason why they are changing tax preparers? By their choice or were they fired?