The project file is just XML. Why not write a Python script to create the XML file you want? I wrote myself an AWK script to do that, and it worked well.
I don’t use the project panel much any more–only for “stock” help files and such that I always want to be able to get to. For “project” file searching, I use the Open File In Solution plug-in from http://npp.incrediblejunior.com.