So my question is, can a GFCI be bad and that be causing the wires to not actually be hot? Because if a gfci can shut down to the wires coming into it I may be able to replace the gfci and everything come back on. But if Its not then I'm at a loss
No. A GFI can protect itself and can protect any outlet down stream from itself. Meaning it can turn itself off if a fault is detected or it can be wired to turn itself off and also turn off any outlet further down the same circuit. It cannot turn off the power coming to itself.
What you have here is some detective work. It helps to understand how things work and what can go wrong in order to know what to look for. It also helps to have done this kind of thing before.
The first thing you need to do is to try to determine which circuit the outlets are on.
That would be easy if the outlets were working, you would simply turn off breakers until the outlet stopped working. Because the outlets are not presently working that approach won't work for you. I suggest that you try determining which circuits the working outlets are on. That should reduce the number of circuits that the non-working outlets outlets could possibly be on.
You should be able to reduce the number of possible circuits down to 2 or 3.
Then use all other clues you have to determine the most likely circuit.
The first clue would be that unless this is a custom built home, the electrician that wired it wasn't working for you. He was working for the builder who was paying him the least he could. Therefore, the electrician wired it using the least amount of material and more importantly the fastest way he could.
In my opinion a good electrician would put the exterior outlets on a separate circuit. But I am not an electrician working for a builder. Remember clue #1, least amount of material and least amount of time. I suspect that the exterior GFI outlets are on the bedroom circuits with the non-working outlets.
If you look at a regular outlet you will see that there are two ways of connecting the wires. The old way is to strip back the wire, curl it and put it under a screw, close the loop and tighten the screw. That takes time.
The other way is to use the "quick connect" holes in the back. You strip the wire and stick it in the hole. A small spring inside holds the wire in place. Much, much faster. Only problem is that after about 10 years bad or poor connections begin to develop.
Sounds to me that this is what has happen to your home. I suspect that the exterior GFI outlets are on the same circuits that service the interior outlets in the same area and that the quick connect holes were use in wiring the interior outlets.
If it were me, I would begin by pulling the non-working outlets and see if they were wired using the quick connect holes. Using a multi-meter check each outlet for power. Keep in mind that the bad connection can be at a non-working outlet or it can be at the last working outlet on the circuit.
If you find that the quick connect wiring method was used you may as well just go through entire house and rewire all outlets and switches using the screws. If you don't this problem will just keep haunting you until you do.