Thank you. Yes, I understand your goal. Given the information you provided, I don't know why you would have four jacks. I'm guessing that they just used a box that is capable of handling four lines, but not all of those lines are connected. If any of the jacks had short phone cords with modular (RJ-11) plugs on them, that were/are plugged into the four jacks, just unplug them, and that will disconnect the jack(s) from the phone company.
Regarding your question about some of the house wiring not working:
It is possible that whoever built the house didn't connect all the in-wall phone jacks to one main pair of wires. Instead, they might have had several independent wire runs. It's impossible to know without physically being there, with a meter in my hand. So, it might look like this:
----wire from the phone company--->NID (Network Interface Device, the junction box)|---->some house wiring
|---->some more house wiring
|---->some more house wiring
There is no way for anyone here to guess and be able to tell you which wires are which. I suggest that you hire an electrician to solve any wiring problem you can't handle. Otherwise, use only a cordless phone system with a base station plugged into the OBi and forget about the house wiring.