Hi @burhanhagi
To avoid your linker script modifications getting overwriten you can un-tick the Manage linker script

But this may not be the best solution since MCUXpresso will not longer update the linker script.
This section should be included to new project when the FreeRTOS OS is selected. See the below snapshot.


Now, if you do not want to create a new project, you can use the Manage SDK options and select FreeRTOS.


After clicking OK the below window will pop-up. Please consider that the IDE will ask if you wish to update your current SDK drivers, depending on your project and its configuration this could, in the worst scenario some clonficts, just be aware of that.

After buiding, you should see the missing section.
I really hope this could help you
Diego