I found that the best way to do this is to create a scene, and when it is paused, set the onManagedUpdate override this way
@Override
onManagedUpdate(float pSecondsElapsed){
if(mPaused) super.onManagedUpdate(0);
else super.onManagedUpdate(pSecondsElapsed);
}
This way everything works fine, and you can do it at the game level and update the menu layer as usual,
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