Example of overfly
I was working on 12/22 we were to fly ATL-MEM-SGF. When MEM closed for weather, NWA canceled the ATL-MEM flight. We ended up flying the plane to SGF (Springfield) to position it for the next mornings flight. Lucky for three passengers who were transiting MEM to SGF. They had a nonstop flight to SGF in FC while in plied them with wine and warmed mixed nuts.
Hope that helps explain what a overfly is.
Another hypothetical example is a LAN-DTW-ATL flight. DTW closes for weather and the plane just flies nonstop from LAN to ATL without stopping in DTW. Passengers are told in advance, which ususally means the flights is empty or with just a few people.