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We recently moved to a Magento platform and perform the payment authorization for authorize.net and paypal. When the order is shipped, that info is sent from our ERP system back to Magento and then the capture is done.

We would like to do the capture on the ERP system (we do send down a token which we can use). This way the settlement is done in 1 system.

Can Magento just be updated with the shipment information and not have to actually capture the payment?

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In theory? Sure. It all depends on your integration though. Judging by how it currently works, such a change is probably going to require customization.

You could have it run an offline invoice instead of an online one, in which case the invoice is entered in Magento purely for record purposes. Magento won't touch the payment gateway for capturing or refunds in that case.

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