Is there attic space over the lights? I would try to get in the attic next. A common insulation would be for the 2 circuits (in one cable) to go to the closest ceiling light box and one circuit catches the front half of the house and the other circuit catches the other side of the house.
If you can see the wall where wires go down to the panel, you may be able to figure out which wire goes from the panel to a ceiling light. That light would be the first place to check.
You may be able to wiggle the romex enough to make the lights flicker for someone downstairs watching. If you can get the lights to flicker by doing that, the box that wire goes into will be the problem box. It will most likely be a loose/bad wirenut on the white wire.