We're unable to mark the invoice as paid in batch. When you import the invoice via a third-party application, it doesn't include the payment transaction.
That said, it will show as unpaid in QuickBooks.
You can record them manually by going to Create (+), and then Receive Payment.
Also, deleting multiple invoices at the same time is unavailable.
When you're ready to reconcile, you can exclude the duplicate transactions or find match. Here's an article that will help you out: Add and match downloaded banking transactions.
Please let me know if you have any additional questions. Thanks for dropping by.