I am defining several compiler flags in my arduino.json:

...
    "buildPreferences": [
        [
            "compiler.cpp.extra_flags",
            "-DMY_DEBUG=1 -DSW_VERSION_0=1 -DSW_VERSION_1=1 -DSW_VERSION_2=0"
        ]
    ],
...

But the defines for MY_DEBUG, SW_VERSION_0, SW_VERSION_1, SW_VERSION_2, are not changed in the output folders compile_commands.json file.
I have to delete the output folder to get the changes in arduino.json being copied to compile_commands.json.