I am on a Mac.
I'm running the latest MacOS (10.12.5) and latest Evernote version (6.11)
I am viewing an Evernote note with an embedded PDF file.
I right-click and choose 'Open' and the embedded PDF opens in the Preview app.
When I go to make a change using Preview tools, 'Edited' appears in the window title and I am essentially working on a new copy. If I close the PDF it will ask where I want to save the file. If I want I can save it and add the new PDF to Evernote manually.
The old behaviour: it just let me change the file in Preview, close it and the changed PDF would replace the one that I opened in Evernote (the expected and preferred behaviour) It had been that way for years and was very useful.