Quick answer
The control account at the year end is almost never the last return, and AllDone does not expect it to be. It rebuilds what the balance should be: the opening position still unpaid, plus the VAT accrued since the last filed return, plus any filed returns not yet paid at the year end. Where the ledger evidences the payments to HMRC, those are used. Otherwise AllDone tests each sensible "how many returns were still unpaid" explanation and reports the closest, with the residual graded.
What it builds
The walk is an identity you can follow on the schedule: opening balance, plus the VAT declared on each return filed in the year, plus the VAT charged in the ledger that has not reached a return yet, plus penalties and interest posted as journals, less the payments made to HMRC. Adjustments are itemised rather than netted off, so a penalty does not disappear into a timing difference. Where the general ledger is supplied, the payments to HMRC come from the control account's own lines, so the position is evidence rather than an assumption.
Each basis is handled on its own terms
Accruals. The stub period since the last filed return comes from that return's own transaction detail up to the year end.
Cash accounting. The VAT in unpaid sales and purchase balances is brought in, from the VAT reconciliation report where you upload one, from the ledger per customer or supplier where it can be evidenced, and only as a labelled estimate if neither is available.
Flat rate. Each return is tested against the effective rate applied to its own turnover box, allowing for the first-year reduction. The thresholds for joining and leaving are flagged, and limited cost business candidacy is raised for you to confirm rather than applied.
Not registered. A VAT control balance that exists anyway is flagged to confirm with the client.
AllDone also checks the basis on the returns against the basis on the engagement details, and says so if they disagree or if the scheme changed during the year.
How the answer is graded
Within a pound is agreed. Within triviality is agreed with a note. Above that it is flagged, and above materiality it must be resolved. The alternative explanations AllDone tested are shown beside the chosen one. At the Balance sheet recs step the turnover box is then reconciled to the ledger's own turnover, partitioned by VAT rate, which is where a miscoded rate shows up.
If it cannot run
With no returns uploaded, AllDone says the control cannot be reconciled yet and names what would let it. It does not invent a difference, and a check that stood down is never treated as a finding.
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