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I think I just answered my own question. I just found the HMRC stamp duty calculator and it looks like if you are changing your primary residence, you would have to pay all the SDLT but can claim it back (including the amount you would save due to the SDLT holiday) if you sell within three years. So more up front, but you can get it all back, not just the additional 3%.
cjr
I don't think so. You'll pay the second home rate on everything above £500k