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Thank you for your question..
There are two parts to it
1) If the London property becomes your primary residence then on sale of it in the future all gain would be covered by private residence relief and there would be no CGT payable.
2) You can only claim this 3% additional stamp duty if you were to sell the property in London and buy another property that would then become your main residence.
If the Edinburgh property were to be your main residence when you buy the property in London, then sale of it within 36 months would enable you to get a refund of extra 3% stamp duty you would have to pay when buying the property in London.
More information on this can be found under "if you are replacing your main residence" here
I hope this is helpful and answers your question.
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Thank you for your reply.
As you would be owning two properties at the end of the day, there is no escape from this additional 3% I'm afraid. I have explained circumstances where it would be possible to get a refund at a later date. You would only be able to reclaim if Edinburgh property is deemed your main residence before you complete the purchase and then move to London property and nominate it as your main residence.
Just checking to see if you need further clarification/information or have I answered your question.