Link to Customer During Parallel Maintenance
Phase 
Can you exclude existing links to customers in the Treasury Business Partner from the conversion; in other words, can you convert business partners without their customers?
The conversion programs do not provide you with this option, for the following reason:
In the context of parallel data supply, customers are regenerated online when the business partners are processed. As soon as you process a Treasury Business Partner and save the data, the corresponding customer is assigned to the SAP Business Partner.
You will find further information on this topic in SAP Note 398888. Further information on links to customers for the SAP Business Partner is available under Link to Customer for SAP Business Partner.

If you do not want to enter customers during the conversion, you could write a report program to delete the field customer number in the table BP000. In this case, you should remember to save the deleted information in an appropriate place. This kind of report program would delete the link between the customer and the business partner, and references to the customers would no longer be created during the conversion.