Hi Jose
The software does support the management of blanking plugs for connectors where the wires can be present in multiple configuration,
To this this we created 'Technical' assignation and so this assignation option should be used on such connectors (and deselect the Mandatory assignation option). In this mode the system will identify all the possible combinations at the connector and create a technical module code for each, which will be assigned to the connector. Then when you run modular breakdown in to those technical designs the system 'knows' which wire/module combinations are associated to the technical codes and so locates the blanking plugs in the corresponding empty cavities.
Please give this method a try.
Regards
Andy