I am not sure of what you are trying to do here. If you are renaming the project's directory name, I would try:
1) Make a backup copy of your project directory.
2) In the IDE, choose Project > Reset Entry Paths
3) Quit the IDE.
4) Rename the directory.
5) Open the renamed directory folder and double-click on the project file.
6) Choose Project > Re-search for Files.
That might do it. I'm downloading a copy of the Classic tools right now (got to get those latest updates) and this is from memory. Also, make sure that you do not have any absolute paths (for example, C:\My_Project\My_Custom_Headers) in your project. If you do, you need to change those to project relative paths or edit them.
---Tom