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You took the first correct step to see if the payment showed on the application inquiry/reversal screen.
The next step in diagnosing the issue is to open the payment application screen starting a new batch for $0.00 and select one of the customers and select the payment in question by using F3 on the number field. If the payment reference number does not show in the PV list then it has been applied. If it does show, select it and see if you get a message that the payment is already applied in a another batch. If you get that message, note the batch number and take the steps below. If you do not get the message then your auto-apply batch never really happened for some reason and I would suggest that to cancel out of this payment application screen and try the auto-apply process again.
If you did get the message that the payment is being applied in another batch, look on the release AR batches screen and see if that batch appears there. If so and it has an S status, try releasing it again and note if you get a process message stating that an entry was made in the event log. If you do, open the event log and report what is says. If the batch shows on the release batch screen with a B status, you likely forgot to check the release when finished option (or unchecked it by mistake).
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