One of the kittens, the biggest one, is missing. It has been missing, where could it be? I can't find it, and Sheba hasn't done anything different. She isn't moving them I don't think because its been days since that one went missing.

It could have died or been sick so she disposed of it (eaten it most likely), a predator (raccoon, skunk, male cat) could have taken it and killed it. There are a lot of possibilities, and that's why we've all said to keep her inside... but..