I changed my trunk for one I picked up at a parts picker since it was initially damaged. As I changed it, I disconnected the lock cylinder/trunk latch and connected the one from the part I picked up. The car signaled quietly 5-6x times, and then I reconnected the original lock cylinder.

Afterward, the car would not start, and the only way to enter it was by using the metal key. I had a locksmith come out and reprogram the key fob, which allowed me to start the car. My problem now is that the key fob will not work when attempting to open/close doors or the trunk, and the locksmith wasn't sure either since the key fob gives out a signal.
Currently, I can use the handles to lock/unlock the doors and start the car (without having to place the key fob near the start button). I disconnected the car battery and changed out the battery in the key fob with no fix. I have checked most fuses concerning keyless entry, and they look good. Other locksmiths have suggested getting a new key or getting an electrician.

Does anyone have any idea what could be causing this problem?

 

I would suggest adding another key (new or virginized) and see if that works 100%

If you have Techstream it is easy