Refinancing on home with ADU larger than primary

[Benjamin Fishler]

Looking for advice on refinancing a SFH with an ADU on the lot in San Diego, CA as owner/builder who was planning on living in the ADU and renting out the front house.

We went through the entire loan process, got documents signed, appraisal done, closing disclosures, etc -- and at the very end, we were told that the refi loan is getting denied because Fannie Mae guidelines don't allow for ADU's to be larger than the primary house, and the appraiser won't write it as a 2-unit because it's not zoned for such (which is understandable). The ADU is ~1200 sq ft, the primary house is 1014 sq ft. Both the city and county of San Diego specifically allow ADU's to be larger than the primary home, as long as they're 1200 sq ft or less, and it's fully-permitted/signed off.

I feel like this is something the loan agent and lender should have known/told us about up-front, but they said they didn't know. We gave full disclosure on all the specs and specifics on sq footage before starting the loan.

In terms of credibility -- the two units appraised at just over 1.1 million, and we're only looking for ~390K refinance loan. We both make many times more than would have been required in income from our day jobs, have 800+ credit scores, and much more in savings/assets than would be required -- I feel like this should have been a slam-dunk refi. 

So I guess this is both a word of caution when building an ADU until Fannie Mae updates their conforming guidelines, as well as a question to anyone out there who knows of "non-conforming" or loans with good rates for this type of situation that aren't sold to Fannie Mae/etc.

Thanks for any info.