I am in the process of adding a 3/4 bathroom to the upper of my house. The plumber just finished the rough in and all framing is complete. I am now looking at the electrical and I have a issue. There are two lights on a three way switch, but one of these lights falls inside my new bathroom in the wrong spot so I need to eliminate it. I plan on a new ceiling light but it needs to be in a different location. Can I eliminate the light then do what I need to do to the wires (cap), put the wires back in the box, and then put a cover over the box leaving it visible? I will not bury the box or hide it or conceal it. The bath will have its own separate circuit when I am done.
Since it sounds like you have a major remodel project in process you probably have all the walls open too. The very best bet for the discontinued light would be to remove the circuit and electrical boxes entirely. This way you do not need to keep an ugly do-nothing electrical box cover on your wall or ceiling.
Keeping an unused electrical box accessible can be an extra burden if you are trying to put tile on the wall or finish a ceiling. Remove it and eliminate those PITA points.
Yes, that sounds like the correct plan -- just use wirenuts to cap the wires off (as if you were making a connection with them, but with only the wire being capped off included).
Also, make sure the box isn't in the "wet zone" (aka above the tub/shower) -- indoor-type junction boxes are dry-location only!