First I must say that I have no actual experience with the LPC43S67 nor the LPC4370 MCUs.
> I tried commenting out the code in the Chip_Clock_GetRate() but, when debugging with stepping line by line, the function is still being debugged as if it was not commented out.
This is usually a sign that your project setup or debug setup is incorrect or corrupted.
Perhaps it is just out of sync, and a clean/rebuild helps. Because Eclipse projects tend to be somewhat opaque and messy, I often end up creating a fresh project.
Try a simple test here: insert a line containing "#error <some text>" in the source file, and rebuild.
If it doesn't throw an error, you probably have multiple copies in your project.
Onother example of a negative experience I made with Eclipse :
Files (*.c/*.h) are implicitely included in the build and compiled/linked, even if they are only added to a folder a project happens to be located in, and are not explicitely added to the project. This might also happen when you copy a folder from one project to another.
I consider this a critical bug, and one of the reasons I switched to Segger Embedded Studio for my private projects.
> Maybe it is worth mentioning that the code im trying to copy worked on the lpc43S67 instead of the lpc4370 I am working on now.
I don't know if these two MCUs are compatible on that level.
A simple way to check would be to fetch a SDK example for both of them, and compare the implementations of said functions.