This is my headcanon. Don't like it? Don't read it. Don't like my ship? Don't comment.
Sombra - After the incident with Cadence and the Crystal Empire, Celestia had given the wounded Sombra a chance to prove that he could be good, and would no longer use his magic to enslave Crystal ponies and regular ponies alike. She sent him into the care of Fluttershy, just as she had done with Discord before, to be reformed, and attempt to use his magic for good, even though his magic had been gravely influenced when his horn has been sliced off before. After a year or two after staying in the care of Fluttershy, the two grew significantly close, and eventually, love bloomed. After almost eleven months of dating, Fluttershy became pregnant, and it was at that point where they decided to marry.
Fluttershy - After she had been appointed Sombra's caregiver, Fluttershy did all she could to change the once evil and demanding king. Throughout that time, Fluttershy had began to set up her own animal clinic, where she and she alone for a few months worked with some help from Sombra, who at the time didn't much care for anything or anyone. After the 11 months, as mentioned, she became pregnant with Jewel, and was married. Jewel's birth was complicated, and from stress, Jewel, was born too early, and was pronounced dead when she apparently had not made any sounds for quite some time after birth. Eventually, the tiny foal came too, and was to go on and have a happy, yet grumpy life.
Jewel - Born small but with a big attitude, Jewel grew to somewhat inherit her father's Unicorn abilities. She's not able to fully use magic, but is able to somewhat levitate things if she consecrates long enough. This will lead her to pass out eventually. Her wings, even though she was born early, fully developed and are fully functional. When she's angered, her eyes will glow, somewhat like her father's did all the time. She's a very grumpy mare, and hates everyone as she says. She isn't much of a social pony, and prefers to be alone, or with her group of friends.
Cherry Blossom - Cherry Blossom was quite a surprise to Sombra and Flutters, as they didn't plan on having another foal after Jewel, seeing how harsh and complicated her birth was. Sombra was worried for his wife's health, and attempted to convince her to abort the foal. Fluttershy almost considered it, but eventually declined harshly, and became very protective and sensitive over the subject of babies. She said that no matter what, she was going to have this baby, even if it killed her. She stopped working 2 months into her pregnancy, and took a break from anything stressful. She began meditating, and eating more organic foods to keep herself and the baby healthy and stress free. 9 months pass, and Fluttershy smoothly gives birth to a little baby girl. The doctors are baffled when they notice her strangely gradiented pink wings, and sombre hair. They labeled this as a birth defect, and began to do tests on the foal. For two years of her life, she was being tested on, but eventually Fluttershy stopped the tests, and claimed that she was just born that way. She is Fluttershy and Sombra's youngest, but not last foal.
Finally, a family picture. Now, I gotta do the others o w o
Fluttershy, Sombra (c) Hasbro/Lauren Faust
Jewel, Cherry Blossom (c) Me
Without effects: sta.sh/0h3w9vi4ra0