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Also, is there a way to automatically clear these invoices when goods receipts arrive?
This is an application issue of your MM-PUR customizing.
The IDoc is handed over by the IDoc engine to application processing. It is the application that rejects the invoice. You have to see this issue with your MM-PUR functional team so that they set up customizing or prepare a user-exit that allows to accept invoices in this cases. Automatic clearance of blocked invoices has not been possible in older releases. I have not checked if it possible in 4.6. What you can do, is set up a custom workflow that does the job triggered by the goods receipt.
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