"The Envelope" is tricky because it was originally filmed as part of a full episode. It's addition to Missing Pieces and thereby Lost canon, is extremely important. It is likely that that powers that be decided that this was important enough information to alter from the pattern the rest of the mobisodes follow.
Amelia will reappear in the storyline in Season 6.
Ben's time Travel was why he said something to Jack in a Missing Pieces episode. In Missing Pieces' "King of the Castle", when Ben was playing a chess game with Jack, he told Jack he wouldn't try to stop him from leaving the island, but that someday he may want to come back. Then Ben said, "And if that day comes, I hope you remember this conversation." He said this because he had been time traveling from that future time.