Thank you for your query at DoctorSpring. I am Dr.Ratnakar Kini, a Gastroenterologist and I am pleased to assist you.
An upper GI endoscopy never causes pain in the right lower abdomen either during the procedure or after the procedure.
As far as colonoscopy is concerned, there may be some sort of discomfort during the procedure which subsides once the colonoscope is taken out. If you are sedated at the time of the procedure, you will not feel the discomfort even during the procedure. In either case however, there will no discomfort after the procedure is over.
So there should not be any pain two days after the procedures.
One of the important causes of right lower quadrant pain and tenderness is acute appendicitis. My advice to you is get examined by your doctor again to rule out appendicitis.
Hope this helps, please feel free to discuss further.