First, use expanding foam to fill the ductwork below the floor at each register. Just foam block the area near the floor hole with foam.
Then mix up some pre-mix concrete and dump it into the hole in the floor into the ductwork. Fill the duct register hole with the concrete and let it dry. Fill the concrete hole so it is just below the floor level about 1/16 of and inch.
Next use a floor leveling compound and a drywall trowel to smooth off the filled up hole and make the hole-filler smooth with existing floor. Then you are done.
Proceed with your other duct improvements.