Somehow we do not understand each other.
What is your pain to create a download from KNVV with the current information of the deletion indicator, then you mass remove the deletion indicators and set it only to those customers again which are in the sales areas to be archived.
Then you run your archiving
and finally you set the deletion indicators back to those customers in your still existing sales areas like it was before.
Please do not consider to write any custom program to force archiving of the customers if you still have business documents, you are only creating a mess and the next problem in your system