You can select all the files in your project and set the Path Type for all of them in one go. While this isn't a script this does save a lot of time over doing the files individually
I think the best approach to script this would be to look in the .xcodeproj file - the file paths are listed in there. If your project is called MyProject you need to open (either by using Show Package Contents in Finder or just the usual cd in Terminal) the MyProject.xcodeproj directory.
In here you'll find a file called project.pbxproj - open this in a editor that won't mess up your formatting and have a peek around the file. If you search for one of your files in the project you should be able to see how Xcode stores references to the project files.
Look for a section named /* Begin PBXFileReference section */. In here all your files are listed, along with where they are relative to the project, e.g.:
... path = Classes/MyClass.h; sourceTree = SOURCE_ROOT
If you can parse this file you should be able to acheive what you want - but remember to back up the file, otherwise you might corrupt your project.