Client has one rented property and is buying another to rent out. He currently lives in a flat which is attached to a fishery/restaurant which I expect is classed as a mixed use property, not residential. He is also now buying a residential property which he intends to live in as his main residence and then rent out the flat attached to the Fishery. So currently he does not have a main residence but my interpretation is that he would still have to pay the additional 3% SDLT. Does that seem correct?
From the facts you give, if he owns the fishery flat either freehold or on a lease of more than 7 years he could sell that and then claim the replacement of main residence exception on his purchase even though the fishery flat were classed as mixed use (which it may not be if it is a separate dwelling). So I think that he does currently have a main residence but because he is not disposing of it he will have to pay the additional charge on his purchase. However if he sells the fishery flat within three years of the purchase he could claim a refund of the additional charge.