And they certainly did leave en masse after the Revocation of the Edict of Nantes.
There is no evidence that a single Protestant was on board the barges that Carrier sunk.
What we do know is that among the prisoners that Carrier murdered were a large number of prisoners of war taken from the forces of Henri de la Rochejaquelein, who was the commander of the largest army in the Vendee resistance movement.
The name of that force?
The Royal And Catholic Armies Of France.
After the recission of the Edict of Nantes, no one in his right mind would stay in france and let anyone know he was a Protestant. Still, the neighbors knew and turned 'em in to the committees of public safety and agents from Paris.
BTW, this doesn’t mean that France’s central government hadn’t changed some time before the Revolution. There are Jews named among the members of the White Coats who fought against the British invaders in Canada for example. At that time they would most likely have been the only Jews in any army in the world.