Oracle Support tells us (in Note 878976.1) that the system does not support this functionality, although an enhancement request has been logged.
We were in a situation where we had no choice but to un-common some BOMs. We found this script to be effective:
SET common_organization_id = NULL ,
common_assembly_item_id = NULL ,
common_bill_sequence_id = bill_sequence_id ,
source_bill_sequence_id = bill_sequence_id
WHERE source_bill_sequence_id != bill_sequence_id
This script as written will un-common all BOMs. Obviously you can limit it to specific BOMs if you want to be more targeted.