Hi.If you look here, you will see that the self-build VAT reclaim scheme for self-build homes and conversion from commercial to residential accommodation existed as far back as the 1990s though I don't know the exact date the scheme was introduced. The notes in Form 431C refer to converting a commercial building into a dwelling, not multiple dwellings, though paragraph 3.2 in the link I gave for VAT Notice 719 you mentions "a communal residential building". VAT Notice 719 was withdrawn in August 2009 as you will see here. I've made claims for clients for conversions of commercial property into single dwellings only so the fact that you converted the property into two dwellings may have impacted on your claim since there was a commercial element to the conversion.
You cannot benefit from zero-rating if you do the conversion yourself. Instead, you make a claim for repayment of the VAT on the materials you buy.
I hope this helps but let me know if you haTve any further questions.