How can I have my duplex appraised properly?

I bought a duplex in 2009. I live in one side and rent the other. My problem is I only have one mortgage for both properties. I had an appraisal in 2012, which resulted in each side being appraised separately. I am now trying to do a cash out refinance, but the appraiser only looked at the original appraisal, not the most current one and appraised the property as one. Now my refinance may not go through. What can be done, if anything?