I am not sure I understand your question, but it might be easier to answer it if we could see your files.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.
If that .zip file is less than 50MB you can attach it to this support request. Otherwise, you can upload it here:
It sounds like you are saying that you are using the "--export-method" command line argument to tell SkylineRunner to export an instrument method. Please let us know what your entire command line is.
Have you tried exporting the method using the regular Skyline graphical user interface (menu item "File > Export > Method")? If so, is the method that you get from the command line different than what you get using Skyline menus?