Found this technique today, sorry if it's been mentioned before:
Problem: Two overlapping parts where one of them is not as sharp and thus is reducing the quality of the area of both.
Once aligned (of course) -> view two scans (or a many).
Identify the scan that has a poor surface in the area you are trying to correct.
With two or more scans visible, select the area with polygon or rectangle selection that is overlapping and of poor quality.
Turn off (eye icon in the list) all scans except the one to delete area.
Delete key or red X
Continue the same procedure as you make the next scan visible.
It may sound complicated, but it's actually very fast, a few seconds per scan to clean.
P.S. A free lasso tool would be helpful instead of the polygon tool.