Preheat the oven to 375-degrees Fahrenheit.
Use a paring knife or fork to poke several holes into each bratwurst.
Add the beer and caraway to a large skillet.
Add the bratwurst to the skillet and simmer for 15 minutes.
Remove the bratwurst to a cutting board and allow to cool.
Reserve the beer and the caraway from the skillet. Set aside to cool.
Tear the pretzel rolls into bite sized pieces and place them in a large bowl.
Add the drained sauerkraut to the pretzel bowl.
Once cool, chop the bratwurst into 1" pieces.
Add the chopped brats to the pretzel bowl, along with the reserved beer from the skillet.
Stir well to combine.
In a large bowl, whisk together the eggs, milk, mustard, salt and pepper.
Pour the egg mixture over the brat and pretzel mixture.
Add the cubed Swiss cheese and thyme leaves into the bowl and stir very well to combine.
Spray a 3 quart covered casserole dish with olive oil spray.
Spoon the bratwurst and pretzel mixture evenly into the prepared casserole dish.
Cover and bake in a preheated oven for 60-70 minutes.
Remove the cover and continue baking for an additional 45 minutes, or until the center is set and when a skewer inserted in the center comes out clean.