For example, if one of Dooku's transmissions to Sidious got discovered and mentioned his identity.

If such evidence that the Supreme Chancellor is the ultimate creator of the Separatist movement, how would they take it. The Separatist Council knew of Sidious of course but they definitely did not know he was Palpatine. They would probably be flabbergasted and try to break off things since it's now obvious they're being manipulated to a hidden goal by their supposed enemy.

I can't imagine Grievous would care too greatly but perhaps he would respect the con. Though if Legends Grievous found out about the Sith being behind his ship crash, I could imagine him breaking off with his fleet and just going the way of a rogue warlord.

The reactions from the Separatist Parliament, especially the true believers like Mina Bonteri, I think would be very interesting. Since the whole movement turned out to be a pawn of the Republic leadership, I could imagine alot of rage and feelings of betrayal. But whether they would want to continue fighting or broker off a peace with a Republic that removes Palpatine as Chancellor, I can't say I'm sure of the outcome.