Chop raw bacon in pieces. In a large pot over medium heat, cook bacon until crisp. Remove with slotted spoon and drain on paper towels. In the same pot, add butter and diced onion to bacon drippings and cook until onions are tender, about 10 minutes.
Add one-half bottle of beer and continue cooking; reduce by half, stirring occasionally. Stir in chicken broth and cream and bring to a gentle boil. Reduce heat to low and stir. Cover pot with lid and simmer for 20 minutes, stirring occasionally.
While soup simmers, shred the cheese into a bowl. Add flour to the bowl and toss to coat cheese.
Stir remaining beer into the pot of soup. Add floured cheese to the pot a handful at a time, stirring continually until cheese is melted. Season with spicy brown mustard and sea salt, to taste.
