Over the past few weeks, I have grown so frustrated over this feature that I have tried to escape Evernote. I've tried Bear, OneNote, Ulysses, Apple Notes, and Notion. It was easy to get my content moved from Evernote in most cases, but those products are missing a few things I care about: web browser access, document scanner in iOS app, PDF storage native to the app, and tagging/organization. So I feel stuck with Evernote.
Yesterday, however, I downloaded Alternote. It's an alternative client for Evernote on Mac that is cleaner, faster, and does not yield this annoying message when I move notes from my Inbox folder to its final resting place. It's all still Evernote, but Alternote is, in my opinion, a superior user interface.