Simply put, the Americans who were or had fought for the French army were ignored. They could, some did, stay in the French army. They could also secure a discharge from their units and attempt to enlist in the American military.  There were no guarantees that they would even be accepted.

Americans within the Legion considered themselves to be the "advanced guard of the American forces."  They thought they would be met with open arms when the US entered the war but there was no effort by the American government to request allied armies to discharge their citizens. By the time 1917, there were about 10 Americans left in the Legion. These men wrote as a group to President Wilson but were dismissed by the War Department: “The subject of utilization of the services of Americans serving abroad has received the careful consideration of the War Department in a number of instances, and the conclusion has been reached that it is not deemed for the best interest of the United States for the War Department to request the discharge of the Americans serving in the Allied armies.” This led to resentment and anger amongst these soldiers with many staying on with the French army until the war was over.

Still, the men tried to join but they weren't given any type of preferential treatment. Some men failed medical exams due to the wounds they had suffered. Others simply weren't accepted with no explanation.  For those who wanted a commission, it took some time and usually pressure from influential connections.  Soldiers were told that they would have to go through basic training again. Some found it easier to leave France, go back to the US, and join up there. Finally, in Jan 1918, infantry soldiers from the Legion, who could pass the medical exam, could be directly moved into units. The numbers aren't clear on how many but it was in the single digits.

To some extent, it wasn't worth it for the American military to spend much time on these soldiers.  There just wasn't that many. Estimates range from 1000 to about 1200 Americans who joined the French military in some form during the entire war. In April 1917, there were about ten Americans still fighting as infantry in the Legion (More continued to join the legion as other units were now not allowed to recruit Americans.). There were another 120 that were involved in the flying corps. The 170th Regiment, a unit that held a lot of Americans who left the Legion or joined up after the first year of fighting, had about thirty. Probably about another hundred or so spread amongst all the other units. The rest were dead, wounded, or were prisoners. There were far more Americans in the British and Canadian Army.

In Rockwell's book, he gives the numbers that 90 Americans served in the legion. Of those 38 were killed. 6 became officers in the French army and ten eventually were commissioned in the American Army. The Americans who become pilots did better. There were about 180 of them. About 60 of them died. 93 of them were transferred to the American army, which didn't happen until Feb 1918. About thirty of them stayed with the French army.

Sources:

I’m writing a historical novel that has an American character that fought for the Legion. I've read most of the diaries and just about any book about the Legion during this time.

American fighters in the Foreign legion, 1914-1918 by Paul Ayres Rockwell. This book has probably the best overall view of all Americans who fought for France. That being said, Rockwell was a massive racist and he downplayed black Americans who fought for the Legion. Some details are just wrong.

Rendezvous with Death: The Americans Who Joined the Foreign Legion in 1914 to Fight for France and for Civilization by David Hanna.