I think the intent was slightly different between the two. Once More With Endnotes seems to be about versions that have footnotes because they're hard to understand, and The Annotated Edition is about versions that have footnotes to make them easier to understand (or to provide insight into the creative process).
I don't believe that's a useful distinction, however, and it's probably impossible to determine the difference in many (most?) cases. "Hard to understand" is too subjective a concept. I say merge.
Ok, examples moved across, wicks almost all updated (waiting on a locked page request), and redirect created. There's no discussion page to move, so I think we're done here, unless there's someplace I should list this, equivalent to Renamed Tropes.
eta: also did a little de-natterfication and removal of "this troper" from examples while I was in there. :)