Probably there is a misunderstanding.
I was not referring to the background job setup - I believe you that it is properly configured.
However, the job selects documents from table VKDFS - SD index: Billing Initiator, to create SD invoices, so if for some reason there are incorrect entries (incorrect from business perspective), it will take them and attempt billing creation.
There is a very informative note, which explains the concept of worklists and how the reorganization report, which I suspect as a culprit, works 128947 - Correction of SD document indexes with RVV05IVB. If you have not come across it, I strongly recommend that you read it.
If the billing relevance for an item category was changed (from ' ' to 'A' for example) after some documents were created, this would not affect them and they will get 'completed' status after goods issue. But if you run billing index reorganization, they will appear in VKDFS and you will be able to invoice them.
If somebody made changes in Set Updating of Partner Index, he would probably run this report as well.
It is possible that these documents were just blocked for billing, but I find it very unlikely that this was the designed and approved solution at that time.
Checking VF04 with selection for blocked documents is typically a part of the weekly/monthly tasks for the billing department, so somebody must have seen them them years ago - if not the users, then the auditors would have noticed.
Not to mention that you cannot archive deliveries in process.