"ok, let's think this through... First of all, they must not know about us. None of us were kidnapped, but our mothers where. We don't really know if our fathers have been kidnapped, but it is possible. I doubt that the villains found the elements- we would probably know by now. The princesses do have plans in place for if something happens to them. We need to get to Canterlot either way though. I know the elements of harmony are kept there, so we'll need to retrieve them." She said.
(Ok, so I'm thinking they can be like new elements of harmony, since each one has at least one kid. Honesty would be Orchard, Magic would be Starburst, Kindness would be blossom, Generosity would be Beauty Hearts, Laughter would be Strawberry Pie, Loyalty would be Rainboom. Cookie, if you want to have a child of Rainbow Dash or Apple Jack, you can have that element since you don't have an element and I have two. If y'all want to swap it up some, there is only one child of Apple Jack, Rainbow Dash, and Rarity, so those will likely stay the same. Pinkie has two children, Fluttershy has two, and Twilight has three. I just want to make sure everyone has one element.)
(Also, maybe Flurry Heart wasn't captured, somehow followed the villains and was able to get the alicorn magic from them before the villains took it? And maybe she was like told to keep her mothers, give Celestia's to Nova, Luna's to Dawnlight, and divide Twilight's between her children, so its easier to control, and if one of them gets captured, they don't loose all of there magic??)