First, prep the beans. Ideally, pre-soak the beans for at least four hours in a 1% salinty water. Then drain and add to the pressure cooker along with plenty of water, at least enough to cover by 1" or so. In a cheese cloth or cloth bag, put half the onion, some carrot and celery chunks (or celery greens) and a few cloves of garlic. Add some peppercorns and pepper flakes, but only a pinch or two of each. Add a small piece of kombu. Tie and add to the mixture. Heat to high pressure for the appropriate time for the type of beans. Allow pressure to release naturally, and check for doneness. If not done, repressurize to low pressure for a few minutes and then allow pressure to release for 10 minutes before releasing the rest of the pressure.
While that cooks, peel and dice the remaining vegetables and place in one bowl. Vegetables for this part include one carrot, one celery rib, and the remaining half of the onion. Peel and thinly slice the remaining cloves garlic and also add to the bowl too.
When the beans are almost done, warm 3 tbsp olive oil in a large stock pot over medium heat. Add the vegetables and sauté until soft, about 10 or 15 minutes. (Resist the urge to add salt – saurkraut can be very salty on its own.) Add the thyme and 2 cups broth. Stir well.
Drain the sauerkraut well, allowing to drip.
Gently add the beans and the sauerkraut. Stir until mixed and gently simmer on medium heat for about 10 minutes. The soup should be very hot. Check for seasoning and ladle into soup bowls. Serve with a crusty bread.