I struggled with the very same problem for months now. I waited for an macOS or an Evernote Update desperately. Nothing happened and I wondered, if I am the only user with that problem. So I tried to find a solution on my own. I was led to sites where it was about a problem with the ScanSnap driver. Others said it is a security problem as the existing replies in this forum.
But, it seems just that in Sierra it is not possible to edit a PDF file that is located in the Library folder. It has no relations to Evernote or ScanSnap or whatever. Regardless of which PDF file I use, whenever it is copied (with finder, not with Evernote) into my Library folder, it cannot be manipulated. On that page they discuss this problem: https://forums.zotero.org/discussion/61014/macos-sierra-papers-protected
I did not find a way to tell Evernote to use another path for its datastore, as it is suggested in that forum above. You can, however, move it and create a symlink to the new location.
SOLUTION:
- close Evernote
- open finder and navigate to /Users/<username>/Library/Application Support/com.evernote.Evernote/accounts/www.evernote.com
- there you will find a folder that is named as a random number
- move that folder to any other place on your disk using finder (I used the Documents-Folder and a subdirectory called EvernoteArchive
- now open terminal
- navigate to the /Users/<username>/Library/Application Support/com.evernote.Evernote/accounts/www.evernote.com folder
- create a symbolic link with the command:
ln -s /Users/<username>/Documents/EvernoteArchive/1234567 1234567
(replace the path according to your new location and the number with the actual number that your folder is named after)
- In finder you should see the original folder with a link icon in it
- you can now open Evernote again and it should work as you are used to