Hello everyone,
I recently became a premium user and this issue start happening to me. I am really surprised that this bug isn't resolved since last Summer! I hope that Evernote developers are aware that this is a real deal breaker for us paying users. This is some basic functionality which we should not even discuss.
I resolved my problem by copy-pasting the conflicted notes into a new ones, since nothing else seems to work.
Happy New Year to you all!