Lets say for example that I had two different folders with a part in it named "screw.sldprt". Each of the two files has different configurations in it, and both are used in the same assembly. If I were to do a pack-and-go of the assembly, how would SolidWorks handle that? Would it copy both files? Or just one?

I recently did a Pack-and-Go for a customer, and the assembly is old enough that it is from when we used the standard SolidWorks toolbox components. We stopped using them because there were so many different hardware files with the same name and different configurations that it was confusing. I ticked the "include toolbox components" box, and I added a suffix onto all files so that it wouldn't get mixed up with their own toolbox components if they used them. They informed us that they were having problems opening the assembly and that it wasn't finding hardware even though the hardware files were included. I tried opening it and got the same problems.