If one of the blacks labeled as line in your drawing powered a load and the other did not, then it matches my thought that one is from your breaker and the other is just some downstream part of the circuit.
Wires going to ceiling lights that are pre-wired for fans typically have a red/black/white/ground conductor. I believe red is typically used for the light part of a ceiling fan and black for the fan but I would not be surprised if this were not always the case.
Is it possible that the other ceiling light(s) are pre-wired for a ceiling fan? Red is also used as the traveler wire in a 3 way switch circuit. Could it be that the house once had a 3 way that was disabled? Is there a switch in that general area that does nothing or disables the light (meaning if turned off then you can no longer turn on the light from this other switch you are working on)?
In the event of a 3 way, this thread might help: