Is the tip of drilling 6 one-inch holes in a rafter below and above an obstruction like a skylight OK if the rafter is a 2" x 4"?

Consult a structural engineer before drilling into a 2" x 4" rafter.

Removing a 1 inch section from the middle of a 2" x 4" rafter will only leave 2/3 of the material left in place at most. Air Vent suggests consulting with a structural engineer to find out if this would be okay and get some general information on this modification on small rafters.