Hi,
Seems like some physics components are disabled for the new primitive.
In order to simulate the physics, it is necessary to add some physics components in the original USD (or in the loaded scenario, but this way does not store the changes): PhysicsAPI, CollisionAPI, MassAPI:mass
Use the tab PhysX Properties and add those components with the comboBox Add Prim Component. Also, set up the mesh of the collision components (and, change the mass of the body if you want). After that, save the changes File > Save
I reproduced your steps, enabling those components for the mesh (Body_217) of the Isaac/Props/Flip_Stack/bearing_pin.usd asset (also, I disabled those components for the blue block just for test) and everything is working according to the physics law (except the blue block because its components are disabled).
