In our seemingly never-ending issues with my wife's 2014 Civic EX-L, we recently had an issue with her alternator not charging the battery (new battery put in 3 weeks ago and was fine until this).
She got the "Check charging system" indicator and battery symbol light on the dash. I measured the battery and could see the alternator was not charging the battery (voltage 11V and dropping).
Soon the car just stopped working with all systems reporting failures. The alternator had already been replaced twice in the last year.

Our mobile mechanic that sold and installed the alternator (Denso) came back out (still under warranty for 10 more days) and wasn't happy about it but removed it and took it to get a replacement.
Came back, put it in and -- no charging. Battery at 11V instead of 13-14V charging. Soon the car just dies as the battery is sucked of life without being charged.

Perplexed, he checked the output of the alternator AT the alternator and nothing (the big post in the center of the alternator that is covered with a rubber cap).

Then, starting wiggling wires and noticed that the two fat wires that attach to the side of the fuse box (in the engine compartment) when wiggled, would make the alternator charge the battery.

Those two fat wires are part of the positive battery terminal harness. I think they go to two big metal tabs that are screwed down in the fuse box.

My question is, is there a relay or something in the fuse box that turns on/off the alternator output to the battery or how does the alternator know when to charge?

Changing the fuse box seems silly considering there is a wiring bunch under the fuse box with hundreds of wires. But replacing those two fat wires that attach to the side of the fuse box seems worthwhile trying.
I assume those two fat cables attach to the tabs in the diagram below with red arrows?

Anyone ever done this or had this problem?

red arrows point to metal tabs with screws that hold them down.

 

These should have an ELD that the ECU uses to tell the alternator to run in full power mode instead of fuel saving mode that may have gone bad somehow and the ecu is not telling the alternator to charge in full. It may be removable. Do you have any check engine codes ?

You said he checked voltage at the alternator itself, how much was he seeing ?

 

There is an update. It seems someone who worked on the car in the past broke a screw in the fuse box and jerry-rigged a fix that was (I believe) causing an intermittent issue of the battery not charging.
In the diagram I included, just to the right of the two posts (notated by the arrows) is another set of 3 posts that are secured by long screws. The middle one -- someone has replaced the original screw with a larger screw that didn't fit the hole and added a bunch of washers to. Total kludge.
After removing that I could see the original screw was broken off down into the hole where the threads are. The original screw, when tightened, would compress two blocks of metal so they make contact. With the kludge screw, nothing was securing anything that the two blocks of metal weren't always making contact, causing the alternator to not charge the battery sometimes.
What needs to happen is the broken screw get drilled out and the hole re-tapped with new threads and new screw put in. But in the meantime, I tapped new threads in the upper metal piece so the screw would go down far enough to touch the broken off screw and complete the circuit. It's confusing if you haven't seen the fuse box in person, but the point is some shop broke something and tried to hide it by kludging a fix.

So, right now, it seems to be working. BUT, I suspect that the alternator now may be charging all the time, which isn't good either. I need to do some monitoring of the battery voltages when the car is running to see if it ever drops from 14V down to 12V.