It's good that you've already started collecting references, because you have evidence showing a history of good work to back up your position. What you should do is continue the paper trail: Write a polite letter to your supervisor expressing your surprise at the contents of the evaluation, based on your previous evaluation and the recent references from doctors (attach copies of these to your letter). Conclude the letter by telling her that you look forward to discussing the matter with her. The ball will be in her court, as the saying goes. What you have to do next, if anything, depends on how she responds.