What does a pediatric gyn md does at a visit for a 12 yr old that misses appt? Do they do paps?

It depends. It depends on symptoms and if they are sexually active. They may do a pap...Check for sexually transmitted infections, do a pregnancy test, discuss safe sex possibly, they may check a urine for uti. Again it depends on the presenting complaint.
Not typically. A 12 year old usually would not visit an OB unless there is a specific issue, like sexual activity, birth control, infection, or other concern. There usually won't be a thorough internal exam with pap until the late teens. Generally there is a thorough external exam, and discussion of safe sex, possible prescription of birth control, and a wet mount done (for bacteria) if indicated.