Ever since the end of the war, Twilight and her friends had terrible PTSD. Eventually, Starlight and the other ponies came down with various conditions that threatened their health.
Rainbow Dash had dislocated both of her wings at Wonderbolt practice, and had come down with pneumonia. The disease was so bad she had to be kept in an isolation room, but she was taken only three weeks after being transferred. The Wonderbolts were in massive sorrow.
Fluttershy had developed a weakness in her immune system, which led to her constantly catching stomach viruses. Eventually, she contracted a virus that somehow caused her to choke on her own blood. She died painfully, and was mourned over by her animal friends.
Rarity had caught Haemophilia, and was told to be extra careful when out and about. However, during a short hike, she tripped and cut her hoof on a sharp rock. No matter what the doctors did to stop the bleeding, they couldn't do anything. Rarity died three days later from blood loss.
Pinkie had developed Type 1 diabetes, and had to watch how much sugar she was taking in. She was doing great, until two months later. She had forgotten what her limit was, and accidentally took in too much. Maud saw her pass out and go into a coma. No matter what her sister did, Pinkie was through.
Applejack had contracted E-Coli. Constantly, she was sick and throwing up. This got so bad that she couldn't keep anything down at all. Due to the severity of her sickness, she died from starvation.
Starlight had developed retinal cancer. She lost her sight three weeks after being diagnosed. To make matters worse, the cancer was rapidly spreading. Eventually, it became critical and attacked her organs. Starlight passed away two weeks after being admitted to the hospital.
The Young Six took the matters into their hands, and took up the now open jobs as teachers at the School of Friendship. This is what they were trained for when working as aides.