Since the 6.9 Evernote update (direct, not thru App Store), I have lost multi-page PDF annotation capabilities and sometimes even single page PDF annotation capability. I have sent in a support request, which was addressed very rapidly (thank you!), and I was told that this is, in fact, a feature to protect my work. The tech let me to believe that it was always a feature and that my experience (which has been long-term, I assure you) was the bug. But it was a very useful bug to me, since I use EN to present college lecture PowerPoints which have been converted to PDF and loaded into EN expressly for annotation. I was hopeful, since the tech also told me the next stable release (presumably 6.9.1, which I now have) brought my "bug" back. Um... nope.
Please bring this "bug" back! At least allow us to select the option "at our own risk."
Now, to be fair, I do not recall doing any annotation immediately post upgrade to macOS Sierra, so I cannot pin this apparently re-enabled feature on the EN 6.9 update definitively. But still, my request stands: Please bring this back. Why can I do it on iOS and not on macOS? (Which actually might indicate its a Sierra issue.....)