I’m trying to punch a hole through a cone ( think of an inverted paper coffee cup). I’ve drawn the cone and attempted to punch a cylinder of the correct diameter through the cone. I used Intersect with Model and then withdrew the cylinder. The resulting hole leaves a gap between the two walls of the cone.
First thing I did was to reverse the faces on the cup. Not that it was needed, but it looked better then. After that I put the tube where I think you mean it to go, and selected both objects, then did the intersect with selection. Then I exploded both groups, and deleted the parts that weren’t needed. I imagine there is a faster way, that doesn’t use the solid tools Subtract, which only comes with SketchUp Pro.
In addition to what you found (select all the faces and reverse them from the right-click menu), you can right-click reverse one face, then right-click Orient Faces. That should make any connected faces reverse if they need to.