VA Loan Zoning Requirements

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I just signed a contract for a foreclosed duplex at Norfolk, VA using my VA Loan. It's going to be my very first investment and it'll allow me to have the other side pay for my mortgage while me and my wife live in it for free. Everything's going great, the seller agreed to pay about about 95% of closing and all major repairs and it appraised $3000 under market value. Until my loan officer told me yesterday that because the appraisal found that it's "Legal, non-conforming to zoning (Grandfathered)" it may affect the property's eligibility with VA due to zoning issues because if it burns down it could only be rebuilt to a SFH. I'm about to find out today what VA will say about it. I'm thinking that's bogus, I'm sure there's more to zoning than what I know but how would VA consider that non-eligible when it's a residential property in a residential area, the only thing is it's a duplex. Even then, if they usually give mixed use properties a pass anyway why would this one be any problem? Does anybody have any experience with this? The atmosphere's really tense right now. I read the handbook for VA Loan guidelines but I can't understand how this could affect the property's eligibility. The only difference is it's going to be rebuilt as a SFH if it burns down, it's still going to be residential no matter what. As far as I know I'm capable of paying the mortgage myself with or without the tenant.