Hello,
If you need to make any manual changes in the linker command file, you can disable its generation by settings the "Generate linker file" to "no" in the 'Build options' tab of the CPU bean inspector.
Then the linker command file won't be updated by PE anymore. However, this might be a problem if you will change some settings influencing the linker file afterwards. In that case you would need to backup the .cmd file with your changes, re-enable the linker file generation, regenerate the code and make the changes again.
best regards
Petr Hradsky
Processor Expert Support Team
UNIS