Your question title is too long, it should be the actual question.
Are you saying Repair Geometry didn't remove the bad shapes as it is supposed to?
It cannot be identified that whether Repair Geometry has removed the bad shapes or not as after repairing the file gets corrupted. It cannot be added to arcmap, showing error in datasets.
Sounds like the attempts to repair left what remains of the file useless. There is no guarantee that repair will produce a useful file
Checking and repairing geometries—Data Management toolbox | ArcGIS Desktop