System Datasource - META DATA Sync with Catalog->Systems

We had several instances where System datasource metadata was out of sync with System→Catalog for several tables. When we tried to Import metadata, it just imported missing fields into system datasource but index was not updated. That ended with fields out of sequence. Only way, we could get it back in sync, it via deleting all fields in System datasource and them importing from Catalog→System all over again. Please provide an option to over-write and import metadata instead of merging. OR all fields will same name should be completely overwritten including index.