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You can disable the moon's pull gravity so it will still orbit around the earth with no problems and have more mass (The button to do that is in overview,interactions it's called "Pull others" and you can also lock it's radius too)
Objects with low mass losing materials like water is what would happen in real life, seeing as they would not have enough gravity to keep the water stable. So Universe Sandbox is simulating that.
I think you can turn on prevent gas loss in simulation settings. That might the prevent the loss of water but I'm not sure if thats in the spirit of terraforming...