Archived Cliniko invoice is still open in Xero

Archiving an invoice in Cliniko is a tidy up inside Cliniko. The article that tells you how to do it opens by finding the invoice you need to remove, and it says that any payments attached to that invoice are archived with it. It does not mention Xero anywhere. That absence is the whole problem: a reader following those steps correctly is not told that the other half of their ledger is untouched.

So the practice ends the day with two systems that disagree and nothing that looks like a failure. Cliniko no longer holds the invoice. Xero holds it, the payment against it, and every posting the two made on the way through.

An archived invoice that was never paid leaves an authorised invoice in Xero that ages quietly in accounts receivable, so the practice appears to be owed money nobody is chasing. An archived invoice that was paid is worse, because it touches two legs at once. The revenue leg keeps the sale: in the canonical allied health template a private clinic invoice sits in account 400, Clinical services, private patients. The settlement leg keeps the receipt against a clearing account, and that balance no longer represents anything a funder is going to pay.

The bookkeeper source lists the same three consequences from the other end: accounts receivable that overstates what is owed, clearing accounts that do not return to zero, and a larger bill when the accountant has to unpick both before a BAS or a tax return. None of the three announces itself; they surface when somebody is trying to close a period.

Where the answer is a void, the order is not optional. Xero refuses changes to an invoice while a payment is applied to it: Zanda's export article states it as no further changes being permitted once payment is applied, and Cliniko's failed sync article says the same thing from its own side, that Xero locks it out of sending any changes over once the invoice is marked paid. So the payment comes off first, and the invoice will accept the void only after it does. Where the invoice falls in a period that has been locked or a quarter whose BAS has been lodged, the correction is a larger question than the order below, and a document date before the lock date covers what Xero will still take.

A funder invoice that was marked paid in Cliniko before the money arrived posts a receipt into a clearing account, and the canonical allied health template gives each rail its own: account 100, Medicare clearing, is one of ten. Each is a bank type account, posted at the BAS excluded tax type, so the movement is a settlement movement and not a sale. The tax treatment lives on the revenue leg instead. Which account the receipt lands in is a Cliniko setting: a payment type can be pointed at a specific clearing account in Xero, and anything left unmapped goes to the default payment account on the integration.

Which is why an archived funder invoice shows up as a clearing balance that will not come back to zero. The receipt is sitting there waiting for a deposit that will not include it, and every later reconciliation of that rail is out by the same amount until somebody removes the payment. A balance that will not clear has its own page: what to check when a clearing account will not clear.

Ledger Map holds one standing map for the practice, approved before anything syncs, and posts one balanced document set per deposit so there is one exact match left in the bank feed. An invoice that stops appearing on the practice system side is a difference rather than a silent gap: it becomes a question with the invoice, the payment and the deposit it belongs to shown together, and the practice decides whether it is a void, a credit note or a housekeeping change that needs nothing.

The account codes on this page are read from the canonical template the practice starts from, the same one behind the chart of accounts a practice approves at setup. The Cliniko integration page covers the rest of what does and does not travel between the two systems.