Upload models please
Without the model to review I would suggest this,
- If you used hole wizard before you copied the parts all you need to do is change the hole type in the second model.
- If you added the holes in the assembly, verify that the hole wizard feature is in the part itself, edit part first then add holes. if the hole wizard feature is below the parts in the feature tree then this could be where your problem lies.
Hope this helps.
I just went into the base part, and had the tapped hole go through one body, then added a drilled hole to the other body. Not as elegant as a single feature solution, but it worked immediately, and gave me control over the drill size (and therefore fit) of the hole.