Sorry for the delay, Marc, but I have been out of town and could not get back to the conversation.
I find that the skin model you have for the upper skin is very poorly defined and Creo is having trouble healing it. Again, I am no expert on the import data doctor, but in general, it keeps failing to thicken or offset consistently. Someone else may have better luck with it. In theory, you should be able to do a simple 2mm thickening and create the hole feature. I find the IDD very frustrating!
However, to get back on subject, the arcs in the bottom of the upper skin model are a semi-circle by definition. Therefore, you can create an axis on each of the bolt recesses by simply clicking on the arc. There are also endpoints (vertices) on the arcs where you can pick 3 vertices and define a plane (or the axis and 1 vertex). On this you can define a sketch you can revolve to make the feature you are looking for.
Here are some images as to what you can do:
Again, I am not sure what you are looking for as an end result. Just know that there is limited interaction between solid features and surface feature. If you need to blend this somehow, I recommend working with surfaces but the errors in the original import model will give problems with the solidify feature or thicken feature.