Well, you don't have 2D arrays, just two files. If you want to compare entire lines, you can work on 1D arrays, one line/element.
Here's a quick attempt, see if it can give you some ideas. I use strings as inputs and outputs. You can easily change it so it read and writes your text files instead.
Many things could be improved if we had more information. For example do you know if the lines are always sorted?
(I have absolutely no idea what you were trying to do your VI and why you even attached it. It makes no sense at all and contains way too much code for such a simple task. It is also extremely inefficient because you constantly resize arrays).