General Flynn is completely safe. He's one of the top figures in the plan. The only reason that he plead guilty to a crime he didn't commit was so that he could be part of the Special Counsel without leftists viewing it as partisan. Mueller has more than likely been part of the plan the entire time.
Kinda strange though. Peter Strzok was the one who interviewed General Flynn. He knows that Flynn didn't really lie. So, at any point he could have leaked that information and blown the entire cover of the Special Counsel. Wonder why he chose not to.