@mrhutchinsonmn I'm not an expert on this code and when I get into a situation like yours, I suspect a corrupted file. So I download the MySensors code again.
Yeah it's a pain because you have it all configured. To minimize that pain, I create shell script to run the the configure program. I also keep my source files in a different directory from MySensors. When I go to compile the code, I copy the source(s) to the directory(ies) to where "make" expects it(them).
Sometimes, for me, I've bolluxed things so badly that I reimage the RPi and really start over! I try to document exactly how to start over.
I admit, it's not efficient nor elegant, but I eventually I get a configuration with which I can live. Documenting what I do is key!
@NeverDie DipTrace stores all components with the project file, so you can open it on any computer and extract components from Schematic or PCB as a library. Also it automatically saves all project components into design cache, which is immediately accessible as a library with all its functionality.