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would love it if once payment has been made exclusivly through the plugin that it would update the woocommerce books 

Hello You can generate payment link for our jobs through your job sheet, clicking Generate online payment link, which will be a WooCommerce payment link and can be paid through payoneer chehckout page. 

And once you generate a payment link for WooCommerce that is deducted from Job's balance, but if for some reason that link needs to be canceled you can check Payments section in RepairBuddy to deactivate that link. So you can generate a new payment link.