Following some more testing, I discovered that you can move the folder and it will continue to use cached files for a while.
After a restart of IIS, it did discover the new location of the files but how does it arbitrarily choose the path to use?
IE - I put the files into webroot\cgi-bin\aspuploader, but as well I had an old version of the files in webroot\aspuploader-old.
The script automatically picked up the aspuploader-old\resources\uploader.js file, rather then looking in the same directory that
<!--#include virtual="/cgi-bin/aspuploader/include_aspuploader.asp" --> that is called from.
What if for say testing purposes, I wished to have two different versions installed on the same machine, but in different paths? How can I tell the script where to look for ALL related files, or is this not possible?