The reason that your manual invoices are still in Past Due status even though billing information and collection method have been updated is because the invoice is still in Manual status. Changing the subscription's collection method does not impact existing invoices, so they will remain under the same collection method configuration as when the invoices were generated.
This means that in order to collect these past due Manual invoices, you will need to manually collect the payment. To do this, open the invoice --> Click Invoice Actions --> Select View Hosted Invoice --> Click Make a Payment. Review the billing information to ensure that it's correct --> Click Pay Now. The customer will be charged for the invoice and it will close and update to Paid status.