Just to provide an update, I have figured out (in an initial test) how to concatenate (merge) two gcode files and print them. My software workflow includes Simplify3D, a text editor, and GPX. The hardware I am using is a Flashforge Creator Pro. My original assumptions on what GPX was doing interms of overwriting presets in Simplify3D was incorrect. GPX just converts the gcode that is their but needs to know what the target printer is.
The process entails slicing a stl in Simplify3D as normal, except remove the entire "ending script"
In a text editor copy and paste gcode contents to it is repeated. In the middle of the file delete the "starting script". You know have one starting script at the beginning and no ending script anywhere.
Run GPX -m R2x [gcode file]
The Flashforge Creator Pro uses x3g that is enough identical to the Replicator 2 that the x3g file (via SD card) printed.
I had to manually remove the first part while the print was in progress so this is just a test. I am now moving onto working on putting in the code to automatically knock of the print. From there I will work to automate the file creation part so I can print 2017 of the same part for my project.
Thanks,
Chris