Cut the ciabatta in half and then each half in half once more (length wise) so you end up with 4 half pieces of bread. Arrange on a baking sheet and bake for about 10 minutes, until lightly toasted.
Set a medium saucepan over medium-high heat. Add the sausage and cook until browned and crispy, about 10 minutes. Make sure to break down with a wooden spoon. Add the flour, stir and cook for about a minute. Stir in 1 1/2 cups milk and cook, stirring occasionally, on low until thickened. Season with salt, pepper and red pepper flakes.
In a medium bowl, whisk together the eggs and 3 tablespoons milk until well combined. Season with a bit of salt and pepper. Melt the butter in a non-stick skillet over low heat. Add the eggs and cook until soft scrambled.
Spread the gravy on top of the toasted ciabatta pieces. Top with the eggs and sprinkle with cheese. Bake for about 10 to 15 minutes. Remove from oven and sprinkle with chives. Cut and serve immediately.