So the premise from the beginning it seems has been that the need is for some few number of pairs of files; mentioning that you had something like 500 would probably have been a good thing to do early on. :-)
Do you have a plan for how to combine the pairs of files into one file with the line of --------- separating them? That seems key to the solution described thus far. There are some not-so-difficult ways, but specifying WHICH files and making sure there are the same number of lines in each…I don’t know, but I hope you do, as this is your problem and your data. Perhaps the regular expression can be altered to avoid the dependency on “n”, but unless you have solutions for some of the other technical difficulties, well, then…
It seems we are getting very close to advising you that you need a programming language to do this more easily.
And yes, people, I do realize this discussion is getting a bit outside the realm of Notepad++ discussion. :-)