If we have an invoice with a partially paid status and want to create an internal document for it and change its status to paid, this cannot be done by setting the payment status to "Paid (manually)".
The solution is to unlink the payment from the invoice, match it again, and when prompted about what to do with the difference, select "Full payment, post the difference".
An internal document will then be created automatically with the accounting settings predefined on the document type. The internal document can subsequently be found in the Accounting - Internal Documents module, where the accounting entries can be modified if needed.