Thanks for the update, Stefan. Their workaround is what I've been doing already. You're absolutely correct about it being cumbersome. I never realized just how often I edited images in Preview directly from EN until it stopped working. Here's to hoping they roll out a fix sooner rather than later.
I'm having this issue as well in the public release of Sierra, not a beta. Any way to get this fixed? I'm running macOS 10.12 and Evernote 6.9. I've disabled all the optimize storage options in Sierra, so I don't believe it's related to that. This wasn't an issue until I updated to Sierra yesterday.