First of all, change qualifiers from activity to contract type in metric designer,
Then execute, publish, clean up historical data, and transfer data from stage to metric store, we can see the old structure still there
It looks like there is no easy solution, the option 1 is to somehow clean up Metric store, the option 2 is to drop metric type and then redo it. Both options are pretty expensive. There is a way to handle it using metric studio tool to remove these qualifiers, then all metrics will removed accordingly. Once republish data, and then old qualifiers will be GONE.