In 4.21, Datasmith preserves Material assignments after a reimport – for example, when you assign a different Material to a Static Mesh, it remembers that assignment and will maintain your change after a reimport. However, it doesn’t remember any changes you make to settings in the Material Instances, like changing parameter values, or in this case, changing the parent Material setting.
This is fixed in 4.22 – In 4.22, Datasmith tracks all changes to Material Instance properties as overrides. I just tried your scenario in a dev build, and after reimport the Material Instance correctly preserved the new copied parent Material I set for it.
If you need it to work in the meantime while you await 4.22, what I suggest is that after you make the copied Parent Material and you make your changes there, create a new Material Instance from that parent and set up its settings. Then assign that new Material Instance to the Static Mesh Actors in your Level or the Assets in your Content Browser. That new Material assignment should get preserved after the next reimport.