Recreated this myself on a server last night. Hoppers will feed "through" the brewing stand until you lock them to actually brew something. The water bottle hopper will never unlock even after all Radstone is removed. The only way to unlock the hopper is to break the brewing stand and replace it. The hoppers will work as normal again until the bottom one is locked. The side hopper will then never unlock.
Recreated this myself on a server last night. Hoppers will feed "through" the brewing stand until you lock them to actually brew something. The water bottle hopper will never unlock even after all Radstone is removed. The only way to unlock the hopper is to break the brewing stand and replace it. The hoppers will work as normal again until the bottom one is locked. The side hopper will then never unlock.