MTD VAT Submission is enabled by default for all Clear Books customers with a VAT scheme. However, you may encounter a situation where old transactions—which you have already submitted to HMRC via a previous system or a pre-MTD return—are being picked up in your current Return when using the include late invoices option.
To fix this, you can temporarily disable MTD VAT Submission to create a "Draft" return. This locks the historical transactions so they are excluded from your current MTD submission.
Step 1: Disable MTD VAT Submissions
To create a manual draft return, you must first switch off the MTD requirement.
Navigate to Settings > Configure system > Toggle Features.
Click on the "Tax & bank import tool" tab.
Toggle off the "MTD VAT Submission" option.
Step 2: Lock the Historical Transactions
Now that MTD VAT is disabled, you can generate a "holding" return for the previous period to "catch" the old transactions.
Go to Tax > VAT > VAT return.
Select the dates covering the historical transactions you wish to exclude (e.g., the period ending before your current MTD period starts).
Click on the "Search for invoices" button.
Crucial Step: Make sure not to include transactions that need to be picked up by MTD returns. Click on the Create VAT return.
This action "locks" the transactions included in this period, preventing them from appearing in your future MTD returns.
Step 3: Re-enable MTD VAT Submissions
Once the old data is locked away, you must turn MTD VAT back on to file your actual return.
Navigate back to Settings > Configure system > Toggle Features.
Select the "Tax & bank import tool" tab.
Re-enable the "MTD VAT Submission" option.
Result: When you run your next MTD VAT return, the historical transactions will no longer appear, as they are locked to the return you created in Step 2.