Hello Mario:
That project you have in the screenshot seems to be for the BSP. The option is disabled because it makes no sense to generate a linker file for the MQX BSP library. As you mentioned, the file is actually referenced from the application.
It seems you cloned that BSP from another board, so you should find a default (not modified) linker file in the path C:\Freescale\Freescale_MQX_4_1\mqx\source\bsp\<Board>\<Toolchain>.
Regards!,
Jorge Gonzalez
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