Index missing occurs because the cAmountDue field cannot be a stored calculation. (It references data in related tables.) Fields that are unstored do not have an index and since Filemaker uses the match field's index to determine which records in AP_Invoice should match to the current record in AP_PaymentItems, it can't find those records in your relationship.
You'll need to find a way to flag your records that still owe an amount due with a stored/indexed field. You might, for instance, add a "flag" field that is just a number field with a 1 in it if there is still a balance due on that invoice. YOu can use a script trigger to update this field everytime you add or edit a record in payment items or any other field in any other table that might alter the amount due for a given invoice.