Non-Profit fraud is difficult to prove unless they are braindead, without releasing a third party forensic accounting report of the non-profit we will really never know.
The reason it is hard to prove is because for the most part the non-profit can do whatever it wants with the money as long as it is spent on goods or services that can somehow be scoped into the idea of charity related. So, no you can't just withdraw a bunch of money to your account, but do you want to take the family to Miami and throw a giant ass party for a week? Sure charter a private jet and call the party a fundraiser and there won't be any legal fraud there.
The past 6 months could have just been scrounging up enough money to replace whatever they did use over time so they can make that donation now and have it all appear to be level. But he could also be telling the truth.