If you create a hole feature on an object based on on sketch, and add bodies from other components in the "objects to cut" section, the hole feature drills holes perfectly.
However, if you move the component containing the hole feature, the holes in the component move properly, but the holes in the other bodies (that aren't in the component) stay in the old position in the component.
It looks like the hole feature uses the absolute (global?) location of the points in the sketch, rather than the relative position of the component.
You can work around this by rolling back the timeline to before the hole, moving the object to it's final location, capturing position and then rolling the timeline forward. But this becomes very problematic if you have a number of different components in an assembly that you have to re-position.
This kind of re-positioning is common when you're trying to finalize a design and it creates a huge amount of extra work.
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