I had the App Store version 184.108.40.2065521 and recently upgraded to Mac OS Sierra. Could no longer annotate. I found this thread and followed the advice to dump my Evernote application and replace with the downloaded version 220.127.116.115520, which is weird because according to the version numbers it's an earlier version. When I launch the download-version Evernote it said it was moving everything. Once it was done, PDF annotation seemed to work ok again.
Where are the files kept in the App Store Version of Evernote?
Where are they kept in the Download Version of Evernote?
Were the files copied over or moved when I changed versions? I can't locate two copies of the files just poking around, but you never know.
It is certainly more convenient to enjoy auto updates using the App Store. Will this ever be fixed in the App Store version or is it a side effect of the sandboxing of App Store apps?