Hi
What you need to do is to switch to the appropriate Generator configuration (..._Internal_flash). The configurations are visile in the Component view and should be pre-set to select appropriate CPU component (notice that there are two - one is for set-up for code in RAM, the other for code in FLASH).
However, when I imported the PWM project, it seems that it's incorrectly set, because when you change the configuration, it does not switch the CPU, which is the component that actually produces the .LCF file. (There is a typo in the configuration name, there is MK60FN1M0.... instead MKDN60.....)
The workaround is to select the CPU manually (you can also see the picture below):
- Invoke pop-up menu for the second CPU component
- Select "Component enabled" option.
- Re-generate the code.

best regards
Petr Hradsky
Processor Expert Support Team