I am having the same type of issues. Neither search, Spotlight nor the Evernote search, will find notes that I know are there. Notes that cannot be found via search have a blue arrow in upper right corner. The rebuild options for both searches will not work. Nor does exporting and the re-importing a notebook that notebook. The blue arrows are still there after reimporting. Only affect "local" notebooks that reside on my laptop. Evernote Support say they are working on a fix but I am skeptical.