Hi Joe,
PixelCNC projects store the tools definitions in them, so any changes to your tool library won't affect them. This is so that users can share project files without requiring that they already have the tools defined in their library. The tool library is just a list of pre-defined tools so that users don't have to keep redefining the same tools for new projects, but the project doesn't rely on the library retaining those tools, they are effectively copied to the project.
Hope that helps!
- Charlie