Hello! Lilith will take back the ocean gems as soon as the mission is completed. However, even if the ocean gems are forcefully removed, the effects could still very well be active. You are welcome to assume they keep their mermaid/sea creature modifications even back at base if that's something you want to play with!

Edit with more information on ocean gems: The modifications itself however will last a maximum of 24-48 hours. But, who knows maybe the ocean gems will come back once they've been refined!