The lava rock is permeable and will let water through as though the grade was never changed. But you could place an impermeable layer on top of the stones angled the right direction to cause water to run off. Leaving them in place probably doesn’t hurt anything either as long as you understand a grade change is only effective to the extent it causes water to sheet away from the structure, and water problems are not from a sub-surface source such as a high water table.
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