Welcome Carolina once again.
From what I understand from your situation, that this 3% additional payment will be required ONLY IF you keep your first main residence and buy the second one BEFORE selling the first one.
If you move out of your main residence (Home A) but keep it and buy another main residence (Home B), you will have to pay the 3% Stamp Duty surcharge initially.
However, so long as you sell Home A within 36 months (increased from 18 months in the March 2016 Budget) of completing on the purchase, HMRC will make a full refund.
The refund applies, in fact, to the sale of any property that has been your only or main residence at some point during the 36 months leading up to the purchase (ie, you don't have to be moving directly out of one main residence and into a new one).
How long you have lived in a previous main residence will not be relevant.
So, if you have already disposed off your main residence before buying the another one, this additional payment will not arise at all. Otherwise, there will be this refund process that will follow.
I am sure this would help.
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