Identify one affected order before changing settings
Open WooCommerce > Orders and clear date, status and search filters. Confirm that you are signed in to the correct site with permission to view orders. Compare one known order number with the customer’s confirmation and the payment provider’s transaction. Keep those private records in your support workspace.
Record when the order last appeared and what changed afterwards: a storage setting, plugin update, migration or restore. A payment at the provider does not by itself prove WooCommerce saved an order. If the checkout never finished, start with the payment gateway guide.
Record the active storage and synchronisation state
Inspect WooCommerce > Settings > Advanced > Features without changing it. Record the selected order storage, compatibility mode, pending synchronisation and any incompatible-extension notice. WooCommerce’s HPOS documentation explains the storage choices.
The selected authoritative storage is the source WooCommerce uses for orders. A second copy can be incomplete when synchronisation has not finished. Do not switch stores of data simply because the other setting looks familiar, and do not delete tables to force a fresh sync.
Separate a display problem from inconsistent data
If WooCommerce displays the order but an invoice, fulfilment or reporting extension does not, check that extension’s HPOS support and version. Ask its maintainer to investigate the affected order through supported WooCommerce interfaces. A direct database query designed for older order storage can miss the record.
When WooCommerce itself cannot find the order, preserve the current database and available backups before investigation. A developer should compare the authoritative and backup stores, related order details and logs. Do not paste table-copying commands from another installation; order relationships and extension data must remain consistent.
Rehearse any synchronisation repair on a protected copy
Follow WooCommerce’s migration and verification guidance for the installed version. Have a developer identify which direction is correct before running synchronisation, then review the verification result and affected order details. Record WordPress, WooCommerce and extension versions so the result has a defined scope.
Test the protected copy with customer mail contained and payment integrations in test mode. Verify a fresh checkout, an existing affected order, refunds in the test environment and subscriptions if used. A matching total order count cannot establish that the same orders and amounts are present.
Get help with the next step
If the evidence is unclear, get help investigating missing orders. Share the symptom and checks already completed so the next step can be agreed.