I'm not sure that this is right. I thought the law had been clarified (not changed) to make it clear that where a jointly owned property is mortgaged, for the purposes of SDLT the liability is assumed to be the proportion of the debt equal to the proportion of the property owned (with additional clarification that joint tenants are equal share owners)
It's all in Schedule 4 of FA2003
http://www.legislation.gov.uk/ukpga/2003/14/schedule/4
[F9(1A)Where—
(a)debt is secured on the subject-matter of a land transaction immediately before and immediately after the transaction, and
(b)the rights or liabilities in relation to that debt of any party to the transaction are changed as a result of or in connection with the transaction,
then for the purposes of this paragraph there is an assumption of that debt by the purchaser, and that assumption of debt constitutes chargeable consideration for the transaction.
(1B)Where in a case in which sub-paragraph (1)(b) applies—
(a)the debt assumed is or includes debt secured on the property forming the subject-matter of the transaction, and
(b)immediately before the transaction there were two or more persons each holding an undivided share of that property, or there are two or more such persons immediately afterwards,
the amount of secured debt assumed shall be determined as if the amount of that debt owed by each of those persons at a given time were the proportion of it corresponding to his undivided share of the property at that time.
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I'll willingly admit that I don't understand legalese and at least one reasonable interpretation is that (1)(b) doesn't apply. I believe that (1B) clarifies where (1)(b) applies (e.g. change in ownership proportions) rather than (1)(b) disallowing the application of (1B) but I'm neither a lawyer nor an accountant and my belief is worth what you paid for it