My soup has seperated. How do I restore it?

I am making a stroganoff slow cooker recipe. It called for condensed golden mushroom soup, and I made one from scratch. To thicken the soup, before adding it to the crock pot, I made a mixture of milk, er and flour cooking until thickened. Well, I got anxious after I added the soup to the crock pot and turned it on high for an hour ( I know, I should never have done that, but I am an impatient vixen sometimes.) and then it separated. How do I fix this? THere is 2 more hours to finish the dish. I only had it on high for one hour.It has been cooking for 4 hours total.