Not talking about Flynn being charged.
But if he says he was asked by Trump to make contact with the Russians, he better have proof. If not, his word means nothing.
Or do you mean they have proof of Trump (or someone else from the White house) being directly involved as well?
Mueller has a mountain of evidence that we don't know about, so he will be able to make it a slam dunk. Flynn is just one cog in that process.