Hello Shaiz,
To keep master data consistent between active and copied planning versions you should to delete the old copied planning versions during the refresh activity.
The active/inactive versions doesn't have a separate master data at 100%. Some master data modifications at 000 level are transferred directly to the copied versions.
Question - what's happened if in the old kipped version you have some master data that are not present in the newly (refreshed) planning version?
Thanks,
Regards, Marius