How do you check whether an HMRC SDLT refund has really been paid and matched to the right property?

Introduction

People often run into difficulty when HMRC pays a Stamp Duty Land Tax refund but the payment reference does not clearly identify the property or claim. That can create practical problems: the taxpayer may not know which claim has been paid, whether an adviser’s invoice is correct, or whether HMRC is still reviewing the repayment.

This article explains how to approach that situation where several SDLT refund claims have been made across different properties, one or more repayments have been received, and the figures or references do not obviously reconcile.

The Question

A taxpayer had made several SDLT refund claims in relation to different properties. Some claims had already been paid and adviser fees had been settled. Other claims were said by the adviser to have been paid by HMRC, but the taxpayer could not clearly match the money received in the bank account to the relevant properties.

There was also concern about whether HMRC had opened, or might still open, an enquiry into one of the repayments. The taxpayer wanted to know:

• whether the repayment had really been made by HMRC;
• which property or properties the payment related to;
• whether HMRC was still contesting the claim;
• whether adviser invoices matched the actual refund figures; and
• what to do where the repayment total did not reconcile with the stated property-by-property amounts.

Nick’s Explanation

Nick’s explanation, put into general terms, was that a payment shown by HMRC as made does not by itself mean there is an active dispute. In his words, the position was that HMRC had simply flagged the case as paid, and there was no current indication that an enquiry had been opened.

He also explained that if HMRC wanted the money back, it would normally need to open an enquiry into the amendment or claim. If that happened, the substantive SDLT position would need to be defended on its merits.

Nick further said that HMRC payment references are not always reliable for matching a repayment to a particular property. In practice, that means a taxpayer may need to reconcile the repayment by comparing:

• the amounts claimed per property;
• any interest element included by HMRC;
• the dates payments were received;
• adviser invoices and credit notes; and
• HMRC confirmation of which claims have been processed and paid.

The important point is that a statement such as “paid” is not the same thing as a full legal analysis of whether HMRC can still enquire into the claim. It is only part of the picture.

The Law

SDLT is governed principally by the Finance Act 2003. Depending on the nature of the refund, the repayment may arise from:

• an amendment to an SDLT return;
• a claim for overpayment relief or other repayment mechanism;
• a replacement of only or main residence refund under Schedule 4ZA Finance Act 2003; or
• another technical basis advanced in correspondence with HMRC.

HMRC also has powers to enquire into returns and amendments, and in some circumstances to make discovery assessments or otherwise recover tax that it says was repaid incorrectly. Whether HMRC can still challenge a repayment depends on the legal route used for the claim, the timing, and whether the relevant enquiry window or assessment power remains open.

If the underlying refund argument is based on the property being uninhabitable or not suitable for use as a dwelling, readers should be aware that the threshold is now relatively high following Amarjeet and Tajinder Mudan v The Commissioners for HMRC [2025] EWCA Civ 799. Poor condition, disrepair, or the need for works will not automatically mean the property was not suitable for use as a dwelling for SDLT purposes.

Analysis

The issue usually has to be broken down into separate questions.

First, has HMRC actually made a repayment? The best evidence is the bank receipt itself, together with HMRC confirmation that a claim has been processed and paid. If those two things exist, it is reasonable to proceed on the basis that a repayment has been made, even if the payment reference is unclear.

Second, can the repayment be matched to a particular property? That is an accounting and evidence exercise. If the repayment amount exactly matches a known claim, the answer may be straightforward. If it does not, you need to check whether:

• the payment covers more than one property;
• HMRC added repayment interest;
• an earlier invoice was wrongly described and later corrected;
• one property has been counted twice in the adviser’s running list; or
• one of the figures being used is gross, net, or inclusive of interest while another is not.

Third, does “HMRC queried” or “HMRC flagged” mean the claim is under enquiry? Not necessarily. Internal HMRC notes or comments passed on by phone can be ambiguous. What matters legally is whether HMRC has actually opened an enquiry or otherwise issued a formal challenge. Until then, a taxpayer should avoid assuming either that the matter is closed beyond doubt or that HMRC is definitely contesting it.

Fourth, can HMRC still ask for the money back? Potentially yes, if it still has a valid legal route to challenge the repayment. That depends on the procedural history and timing. A paid refund is not always final merely because the money has arrived.

Fifth, should adviser invoices be paid before final reconciliation? That is mainly a contractual question between taxpayer and adviser. But from a practical tax perspective, the taxpayer should make sure the invoice descriptions, property references, and amounts are internally consistent before finalising payment and accounting treatment.

Where the figures do not reconcile, that is a warning sign. For example, if the sum of the stated property refunds is higher than the amount actually received, there may be:

• a mistaken duplication;
• an incorrect invoice description;
• a missing adjustment for interest;
• a claim that was assumed paid but was not paid; or
• simple human error in the adviser’s summary.

That discrepancy should be resolved before treating the repayment as fully explained.

Outcome

The practical conclusion is this: if HMRC says a claim has been paid and the taxpayer has received money, the repayment probably has been made, but the taxpayer should still reconcile the amount carefully and confirm whether any formal HMRC enquiry has actually been opened.

A vague statement that HMRC has “queried” or “flagged” a case is not enough on its own to show that the repayment is under formal challenge. Equally, receipt of the money does not guarantee that HMRC can never revisit the claim.

If the numbers do not add up, the taxpayer should not rely on assumptions. The figures need to be traced property by property, including any interest and any corrected invoices.

Practical Steps

If you are in this position, the sensible next steps are:

1. Prepare a property-by-property schedule showing each SDLT claim, the amount claimed, the date submitted, and the current status.
2. List every HMRC repayment received into the bank account, with the payment date and the exact amount.
3. Check whether any repayment includes statutory interest, because that may explain why the bank receipt does not match the headline claim figure.
4. Ask the adviser for a clean reconciliation showing which payment relates to which property and why.
5. Ask specifically whether HMRC has opened a formal enquiry, and if so, request the date and the document or notice relied on.
6. Request corrected invoices or credit notes if any invoice refers to the wrong property or combines properties in a confusing way.
7. Keep copies of HMRC letters, adviser emails, amended returns, and repayment confirmations together in one file.
8. If the refund argument depends on the property being uninhabitable, review the claim carefully in light of Amarjeet and Tajinder Mudan v The Commissioners for HMRC [2025] EWCA Civ 799, because the threshold is now high.

Conclusion

An HMRC SDLT repayment should always be reconciled against the underlying claims before it is treated as fully understood and final. A payment may be genuine even if the reference is unclear, but unclear references, mismatched invoices, and totals that do not add up all justify further checking. The key questions are whether the money can be matched to the right property and whether HMRC has actually opened a formal challenge.

Legal References Used

• Finance Act 2003
• Schedule 4ZA Finance Act 2003
• Amarjeet and Tajinder Mudan v The Commissioners for HMRC [2025] EWCA Civ 799

This page was last updated on 22 March 2026.

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