Hello Bruno.
About your questions:
1) The best way is to generate Processor Expert linker file the first time and then disable Linker file generation:

This way you can make all the changes you want without worrying about PEx overwriting the linker file. About code and variables relocation you can refer to the next document in the community and MCU on Eclipse blog:
Relocating Code and Data Using the CW GCC Linker File for Kinetis
Defining Variables at Absolute Addresses with gcc | MCU on Eclipse
2) Try using the linker KEEP command, e.g:
.my_section :
{
. = ALIGN(4);
KEEP(*(.my_section))
. = ALIGN(4);
} > m_mysection
Attached is a KDS v2.0.0 project for your reference.
Regards!,
Jorge Gonzalez
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