According to the help docu it is possible to archive one sales area only.
Precondition is that only one sales area has the deletion indicator set and the other not, since the archiving program has no selection for division and distribution channel.
The docu can be found here: Archiving Customer Master Data (FI-AR, SD) - Sales and Distribution (SD) - SAP Library
and I am referring to the sentence " If you set the deletion indicatorin the sales + distribution-specific area, the system can archive the customer data from this area separately "
I also derinve this conclusion from the OSS note 1477481 - FI_ACCRECV: Archiving sales area terminates