It sounds like initially after Milo's fight with the other cat he had some redirected aggression which may have spooked Louis. It's true that when cats relationships become damaged, they can be difficult to repair, but it can be done.
Have a look and see if yuo can catch any of Jackson Galaxy's Cat from Hell on Animal Planet - they often run back to backs all day on a Sunday - they've featured a number of cases like this - each of them required a slightly different approach, but there may be some very useful tips for you to try there regarding shared space, and confidence building.
I do hope you can get it sorted, as it must be very upsetting to you to have Louis staying out. You'll be worrying about him, especially witht he cold weather coming.