Duplicate invoices after a Shopify, Amazon, A2X or Link My Books sync: a guide for Xero users

Your Shopify or Amazon sales are in the books twice. Usually two connectors posted the same days, or a settlement was sent again after a settings change. This guide covers why it happens, how to remove the extra copies by hand, what to do when they are already paid and reconciled, and how to void a large batch of approved ones in one run.

Checked against Xero Central, Xero Product Ideas and the connectors' help centres on 16 October 2026.

Why the same sales arrive twice

• Two connectors on the same days. The Shopify integration by Xero, built by Amaka, syncs daily sales as invoices or receive money transactions, either one summary per 24 hours or one per order, and reconciles them automatically (Connect to the Shopify integration by Xero). A2X and Link My Books post one or more summary invoices per payout or settlement. If two of them cover the same period, every sale is counted twice.
• A historical import over days already posted. The Shopify integration can import up to 90 days of past sales. Amaka's own help page warns that a backdated sync may cause duplicates when sales for those days are already in revenue accounts (Backdate data sync).
• A settlement sent again. A2X says that before re-sending a settlement you must remove the original entry, or you get duplicates (How to remove A2X entries). Link My Books names two common causes of a large batch: settlements rolled back and re-sent without removing the originals, and auto-post switched on with a backdated start date (Voided or duplicated settlement invoices).
• Switching connector. Link My Books' migration article says to turn off A2X auto-posting and start Link My Books after the last settlement A2X sent (How to migrate from A2X). Any overlap at the switch date posts the same settlements twice.

The manual way, step by step

1. Stop the source. Pause auto-posting in the connector you are leaving, or move its start date, before you remove anything. Otherwise the next sync puts the copies back.
2. Find the duplicates. Search sales invoices by contact, amount and date range, and tick Include Deleted & Voided so you can see what was already removed (Search for sales and purchase transactions). Link My Books suggests searching by the payout amount and checking the settlement's history (How to identify duplicate settlements).
3. Decide which copy stays. Keep the one your payout deposits are reconciled against, and the connector you will keep using.
4. Delete the drafts. Draft and awaiting approval invoices can be deleted, and several at once from the Draft or Awaiting Approval tab (Delete or void an invoice).
5. Void the approved ones. An awaiting payment invoice can only be voided, one at a time. A negative settlement is posted as a bill, and bills can be voided several at a time from the Awaiting Payment tab (Delete or void a bill).
6. Unpick the paid ones first. A paid invoice needs its payment removed before it can be voided. Remove & Redo deletes the payment and leaves the bank statement line to be reconciled again (Delete an invoice or bill payment).
7. Tell the connector. Mark the settlement as removed in the connector before anything is sent again. Link My Books has a rollback that removes matched payments and voids what the settlement posted; it does not work in a locked period or on an entry edited in Xero (Rollback feature).

Where the manual way runs out

• Sales invoices are voided one at a time. On the bulk void request (255 votes), Xero's reply of 28 November 2025 says bulk voiding is not planned at this stage and points to the API.
• A month of daily summaries is thirty invoices. Per-order syncs are far more. Each one is opened, voided and confirmed separately.
• Auto-reconciled sales are paid sales. The Shopify integration reconciles everything it posts in its payment balance account, so those invoices need their payments removed first, one payment at a time.
• Settlements can be split. A2X and Link My Books both split a settlement that spans two months into two parts; remove both.
• Lock dates stop everything. Nothing dated on or before a lock date can be changed (Set up or remove lock dates).

The faster way for the approved ones: Unapprove

Unapprove is a web app that works with Xero. Its limits first: it does not find duplicates, it does not talk to Shopify, A2X or Link My Books, and it never removes a reconciled payment. You stop the connector and decide what goes; Unapprove does the repetitive voiding.

• Select the batch. Filter by type, status, date range, contact, number, reference or amount owing, so the copies one connector posted can be picked out by its contact and dates.
• Keep a backup. The preview offers a CSV of the selection with numbers, references, dates, totals and amounts paid, before anything runs.
• Void them together. The void-only run voids approved sales invoices and bills in batches of 50, re-reads each one first, and adds a history note ("Voided in bulk") to every document.
• Paid but not reconciled. A separate "Remove payments and void" run removes those payments and credit note allocations, then voids. Reconciled and batch payments are left alone and listed; use Remove & Redo in Xero for those.

What it skips, and tells you why: documents with a payment or credit allocated in the void-only run (why), documents in a locked period (why), and documents for an archived contact (why). Each run has a ceiling on the number of documents; select fewer and run again.

What access it asks for: your name and email to sign you in, read and write on invoices and bills, read and write on attachments, and read-only on organisation settings and contacts. A payments permission is requested only if you choose "Remove payments and void".

Price: free for 14 days, with unlimited previews and three documents processed in total. After that, $29 per month per connected organisation, or a one-off $49 Clean-up Pass for 7 days and up to 500 documents. Prices are in US dollars and exclude VAT and sales tax (added at checkout); the pricing page has the details.

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