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Based on what you have stated my understanding is you will be replacing your main residence but you would still remain joint owner of the jointly owned marital home after the purchase.
This being the case, you would own two properties at the end of the day of the transaction.
Your purchase would be subject to the higher rate of Stamp duty. If your marital home (previous main residence) was sold within 18 months of this purchase then you would be entitled to a refund of higher rate.
More information on this is covered in Figure 1 below section 2.2 here
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A deed of separation would be helpful. This means that the couple do not have to yet be divorced for one of them to purchase a new home without paying the 3% surcharge as the new property would be in replacement of their main residence.
More information on this can be found here
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