This problem is incredibly frustrating and severely degrades the usability of Evernote. This is not the first time Evernote has failed miserably in their QA/QC. At the very least you should be emailing your users to let them know that there is a problem and provide a timeline for a fix. I'm sure the Evernote team is working hard to solve this problem, but you need to do better. Do proper QA/QC before you release. This is a blindingly obvious bug that should be been picked up. If you want my future $$ you're doing to have to improve. There are plenty of competitors out there who are doing a better job.
Adding my voice to this thread. Evernote, PLEASE fix this! It's an obvious and essential function and it is frustrating to not have it. When someone shares a note with me I should be able to move it into a notebook, and changes I make to it should be reflected in both copies (assuming I have editing permission). Please, please, please do something about this!