Interestion question, but I'd say no. At least not as you think. PAR and other "pseudo compilers" simply pack all files needed to run the script into a single self extracting archive. When you run it, the files get unpacked into a temporary directory. So altering the script file might work as long as the temp directory exists. To be sure it always works, you'd have to manipulate the archive itself (which in the case of PAR is simply a ZIP file)!

Anyway, I wonder why you want to store data in your script file. Why not just use an external file like (~/.yourapp, or MyFiles/.yourapp (for Windows))?