If you're seeing an order twice in QuickBooks Online, it usually doesn't mean MyWorks synced it twice - once MyWorks syncs an order, later changes will update that same transaction in QuickBooks, rather than creating a new one.
Duplicates almost always mean a second app is also syncing orders into your QuickBooks company. The most common culprit is Intuit's free, basic QuickBooks connector apps - like the QuickBooks Shopify Connector (previously known as Shopify by OneSaas) or the WooCommerce Connector - which are easy to connect without realizing while setting up QuickBooks.
How to tell which transaction MyWorks created
In MyWorks, you can click the Synced badge for a direct link to its QuickBooks transaction - open it from there to identify the order MyWorks created.
Checking MyWorks Sync > Log, you can search the order number to confirm exactly what MyWorks synced for that order.
Transactions created by other apps will often look slightly different: a different order number format or prefix (e.g. "Woo-1234"), a different transaction type, different products in the order, or text in the memo line; or one copy showing paid while the other is unpaid.
Clicking the More > Audit History option inside of the QuickBooks invoice or sales receipt will show exactly when it was created in QuickBooks, and by which QuickBooks user.
Checking the apps connected to QuickBooks
You can view every app currently connected to your QuickBooks company here: https://qbo.intuit.com/app/appcenter/myapps
Review the list for any other app that imports sales or orders - especially the QuickBooks Shopify Connector (Shopify by OneSaas) or another e-commerce connector.
For Intuit's own connector apps, you can open the Integration transactions page to see the transactions it has created in QuickBooks. This Integration Transactions page in QuickBooks is reserved only for Intuit's connector apps, and can be limited & confusing. No other app adds transactions here.
Resolving the duplicates
Disconnect the other app (or disable its order importing), so only MyWorks syncs your orders to QuickBooks.
Delete the duplicate transactions the other app created - checking the Audit Log or transaction details first if you're unsure which copy to remove.
Going forward, MyWorks will keep your orders in sync without duplicates.
If you're unsure which app created a transaction, or which copy to keep - reach out to our team. We're happy to take a look with you!