Generating code removes my added include paths

Hi, It's my first time using STM micros and the Cube IDE.

Whenever I generate code from the device configuration tool, the include paths I have added in 

properties > C/C++ Build > Settings > MCU GCC Compiler > Include paths

disappear. This only happens after I close the IDE and then re-open. If I don't close the IDE the include paths remain even after generating code multiple times. The generated include paths are still there (../Inc, ../Drivers, ...etc) but the ones I have added are not.

Is this intended behavior and if so how do stop it from doing that.

Thanks