We are not able to add multiple PO's into a single invoice when Goods Receipt-Based Invoice Verification is set to YES and when we try to create an invoice with multiple PO's, system defaults/references only one PO line items(either the 1st or 2nd PO added).

This feature/functionality of adding one or more PO's into single invoice when Goods Receipt-Based Invoice Verification is set to YES has been restricted in the Ariba system.

When this feature Goods Receipt-Based Invoice Verification to YES, we can only add single/one PO into single Invoice. Instead if you need adding multiple PO's into single invoice then you can set the feature Goods Receipt-Based Invoice Verification to NO and submit the Invoice.

This feature SINV-5407:Goods Receipt-Based Invoice Verification in SAP ARIBA B&I also doesn't support invoices for release contracts, invoices for service orders, or invoices created through evaluated receipt settlement (ERS).

Invoicing > ERS Invoices
Invoicing > Invoice Reconciliation
Invoicing > Invoices against receipts with a ship notice ID
Invoicing > PO Based Invoicing