No it won't. The only thing you have to do is if a white (neutral) wire is used for a line or load purpose you must mark it (re-identify it). Wrap some electricians tape around the wire for a few inches at each end is all that is needed. Use red, black or blue tape but not green, grey, or white. I use a small chunk of colored shrink tube for this.
No, I did not miss anything.
The point is - there are 3-wires. So use them the way how you want.
But you miss the point - the Companion Switch requires only two wires but you do have three. So, there is one extra wire for future use.
That was my point - simply relable wires one or the other way.
That is all well and good for the companion switch, but the main switch needs to switch line to load, and I assume one of the two wires on the companion requires a traveler from the other switch, and that traveler takes away a wire from the first box, leaving me only the ability to switch line to load with the last two wires, assuming I don't need neutral to that box, as there are no wires left.
I am sorry for the noise, you are correct, one wire is missing.
No problem 
That is why I make diagrams first when I do this stuff now, I will mess something up otherwise doing it in my head. I hate that feeling when I get done, turn on the breaker, and the breaker turns back off because I didn't do something right 
