Wondering if anyone else is still having trouble with this?
Even when I create a new note with the article title, either by sharing to Evernote from Instapaper, or by using an IFTTT trigger (i.e. add a new note when the article is "liked" in Instapaper), highlights still fail to append. Instead, I am still left with multiple notes: one original and multiple for each individual highlight, all with the same title.