It looks to me like something similar is answered in this question:
What it seems like you could do is keep an MS Excel file that somehow tracks the location of all your scripts, and then use that to generate a simple high-level do-file that calls all your programs (although this may not be how your scripts work). If your folder locations are changing I am not sure how you can completely avoid updating at least some lines of code when something gets moved around. This would at least centralize the necessary updates into one place.