As toolic said, Welcome to the Monastery.

Since you are working with a large number of large input files, let's do some simple tests to help isolate the problems with the code you posted. It will help us if you make a small number of small files for some test runs (and working with the small files may even make the entire problem immediately clear to you). I suggest three files of five lines each, as follows (be sure to include the header lines, if any, in each of these files):

• An "Example 1" file as described in your original post (I don't think this one has headers, but include them if there are any).
• Two "Example 2" files, one for each of the example 2 types that you showed in your original post (don't forget the headers).

We also need some output files. As I understand your original post, you started with two separate programs, one to process "Example 1" data and another to process "Example 2" data, and each of those worked as you expected. Please run each of these programs on the appropriate short sample file(s) noted above, and show us the output files for each of the three input files.

Last of all (for now, anyway), run your combined program on the three short input files and show us the output file that it generates. Hopefully, we will be able to see how this output differs from the outputs from the individual programs.

Once we have the samples in front of us, we will be in better shape to help you get things working the way you expect.