How should I connect a ceiling fan with four 12/2 cables coming in?
2 hot feeds are almost certainly not "in series" - hardly anything in household wiring is, or should be, other than a switch is "in series" with the things it controls (which are in parallel if there's more than one of them.)

So, cap one off and don't worry about it, as they are the same circuit going to the same box. Nobody knows why the original person did that, possibly including the original person. Unless one is already connected to a switch? Have you checked for that (the switch would happen to be ON when you were testing and found both to be line voltage.)

Deciphering poorly labeled wires is tedious but needful. There are various methods which vary depending on your available tools. I like to make use of a multimeter on the ohms setting on (verified) de-energized wires where possible, connect the suspected far ends, see if you get a low resistance, disconnect them and make sure the resistance becomes infinite, label. Or use a 9 volt battery and the volts setting (extra reminder that you have verified that the wires are NOT connected to line voltage by some means, FIRST!)

I am personally not a fan of attaching power to wires going I know not where, and a cheap multimeter is quite inexpensive, really.

One thought on the "fan .vs. light" labelling (other than being ready for fans with separate inputs) is that the "light" wiring may also run to other "light-only" boxes in the garage?