I was enjoying the new release until I discovered this flaw. My primary use case is sending scientific articles to Evernote for reading, highlighting, and making notes.
Legacy Evernote allows me to open the attached PDF in Acrobat, highlight and comment, then "Save" the revised PDF back to my Evernote note.
Presumably it is a local copy of the PDF that I am opening, editing, and saving.
Evernote 10 allows me to open the PDF in Acrobat, but once I am finished highlighting and commenting on the PDF, there is no option to save the revised version in place in Evernote.