Annotating is working perfectly with my configuration -- Sierra v10.12.3 and Evernote v. 6.10 (454267 direct). Can annotate on all pdfs, including those previously annotated.
I've been regularly and intensely using the workaround recommended by @BSR on Nov 10 and have had no issues using any type of annotation (Sierra on 13" MacBook Pro mid-2012). I will be grateful, however, to see normal functionality restored.
After upgrade to Sierra I'm having the same issues as others. Temporary workaround for me is to open the pdf within Evernote by clicking on the header. Since I have Acrobat Pro it opens in that program and I can annotate and save the doc and the annotations are visible in Evernote. I'm willing to do this for a while until Evernote addresses the issue.