For the last two monthly Graphene updates, my default Phone and Messages apps (I'm ashamed to say they're both Google's) have reset to the default Graphene OS versions. Actually, the defaults have cleared. After each of those last two updates, the first time I use each of the Google apps, it asks me to set the default. I agree to do so and it pops me into the default app area for that app and I choose the Google versions. That persists until the next monthly update.