A manual supplier payment can collide with a scheduled debit

The account is paid through another channel
Suppose a supplier asks for an overdue amount and your team prepares a manual transfer. The account also has an automatic debit arrangement, but nobody checks whether another collection is already scheduled.
Two payment instructions could then relate to the same balance. Before releasing the manual payment, establish what is happening through the existing channel and who can confirm its status.
Check the account and payment instructions together
Reconcile the amount owed, then review the relevant debit notice, payment schedule and bank information. Distinguish a proposed collection from one already submitted or completed.
Do not assume the ledger shows every pending instruction. The person managing the supplier relationship may have information that has not yet reached the bookkeeper or payment approver.
Confirm the supplier's intended collection
Ask the supplier whether the manual payment would replace the scheduled debit and what confirmation it can provide. Record the amount, date and account reference in the discussion.
If changing or stopping a debit is being considered, follow the relevant bank and supplier process and obtain clarification where needed. Do not assume a message to a salesperson cancels an instruction already in progress.
Keep one person coordinating the decision
Nominate the person who will reconcile the response with the outgoing payment list. Make sure other staff know which instruction is approved and which remains unresolved.
business.gov.au's record-keeping guidance includes payment and banking records. Keeping the instructions and confirmations with those records helps explain why the amount was paid through one channel rather than another.
Source: business.gov.au: Record keeping
Reconcile the actual result
Check the bank transactions and supplier account after the relevant dates. If both payments occurred, confirm the supplier's allocation and discuss the appropriate correction or refund with the accounts team.
Do not treat a possible refund as available cash until its timing is supported. Keep the duplicate amount visible so it does not disappear into a general credit balance that nobody follows up.
Add a channel check to urgent payments
Before the next manual catch-up transfer, ask whether an automatic debit or another payment instruction already covers the balance. Record the answer alongside the payment approval.
The purpose is to protect scarce cash during a busy payment run. A correct invoice can still be paid twice when two otherwise legitimate processes operate without a shared view.