Hello Michael,
as starting point for the own Implementation could be for new documents the BADI CRM_UPLOAD_BEA_FILL method FILL_DATA. This will be called before the billing due entry is created. Here you can influence the data and make sure that the relevant fields had the same vaule for supressing the billing split. As already mentioned these can only be a piece of advise for your modification/Implementation.
Best Regards
Gerhard