They were reunited by accident, as a teenager Flurry accompanied her mother to see Princess Twilight. At the time Masquerade was still living with the Crystal children and had visited ponyville with Flurry Heart. The disguised changeling and the alicorn had entered sugar cube corner for a coffee. The changeling sensed the connection between the two, the love, friendship… She encouraged the unicorn shopkeep to join them at least while there were no other customers. Flurry and Pumpkin had vague memories of each other.
They bonded, Pumpkin would visit the crystal empire and Flurry would visit ponyville, friendship turned to something else as it often did. Flurry truely did love Pumpkin and was appreciative of her company when Masquerade fled.
Flurry adopted Silkworm, the changeling foal left behind by Masquerade. Pumpkin loved the little filly just as much as Flurry loved her.
When the changeling marched through the Crystal Empire, Flurry was pregnant with Cupid Cake. She agreed to the changelings terms to cause less stress during her pregnancy.
Cupid Cake grew up around changelings living in the Crystal Empire were the changeling hive and the ponies lived together, she was taught the histories of both people and taught that while the changelings had been depicted a villains in the past they were only following the orders of their Queen at the time.