Flanders family's bomb shelter was a bomb shelter located in the backyard of the 744 Evergreen Terrace. It was destroyed by a comet fragment.
When a comet was going to decimate Springfield, the Simpson family decided to hide in Ned's bomb shelter with his family. Ned is too nice to refuse them, but later other citizens of the town crammed to the shelter and the door won't shut. They discuss who would be unnecessary in the new world and it is exactly Ned with his Leftorium. Ned is evicted from his own shelter and sang outside of it. Feeling guilty about sending Ned to die, Homer left the shelter and the whole group of people abandoned the shelter and join Ned outside.
Later, the comet burnt up in Springfield's toxic atmosphere and shrink to the size of a Chihuahua's head. On its decent it pops the Big Butt Skinner weather balloon which flies into the bomb shelter which the weather balloon bounces off and destroying it.