Helper to deep-copy a TerrainData object in Unity3D

TerrainDataCloner.cs

using System;
using System.Collections.Generic;
using System.Linq;
using System.Text;
using UnityEngine;

namespace ZS.Tools
{
	/// <summary>
	/// Provides means to deep-copy a TerrainData object because Unitys' built-in "Instantiate" method
	/// will miss some things and the resulting copy still shares data with the original.
	/// </summary>
	public class TerrainDataCloner
	{
		/// <summary>
		/// Creates a real deep-copy of a TerrainData
		/// </summary>
		/// <param name="original">TerrainData to duplicate</param>
		/// <returns>New terrain data instance</returns>
		public static TerrainData Clone(TerrainData original)
		{
			TerrainData dup = new TerrainData();

			dup.alphamapResolution = original.alphamapResolution;
			dup.baseMapResolution = original.baseMapResolution;

			dup.detailPrototypes = CloneDetailPrototypes(original.detailPrototypes);

			// The resolutionPerPatch is not publicly accessible so
			// it can not be cloned properly, thus the recommendet default
			// number of 16
			dup.SetDetailResolution(original.detailResolution, 16);

			dup.heightmapResolution = original.heightmapResolution;
			dup.size = original.size;

			dup.splatPrototypes = CloneSplatPrototypes(original.splatPrototypes);

			dup.thickness = original.thickness;
			dup.wavingGrassAmount = original.wavingGrassAmount;
			dup.wavingGrassSpeed = original.wavingGrassSpeed;
			dup.wavingGrassStrength = original.wavingGrassStrength;
			dup.wavingGrassTint = original.wavingGrassTint;

			dup.SetAlphamaps(0, 0, original.GetAlphamaps(0, 0, original.alphamapWidth, original.alphamapHeight));
			dup.SetHeights(0, 0, original.GetHeights(0, 0, original.heightmapWidth, original.heightmapHeight));

			for (int n = 0; n < original.detailPrototypes.Length; n++)
			{
				dup.SetDetailLayer(0, 0, n, original.GetDetailLayer(0, 0, original.detailWidth, original.detailHeight, n));
			}

			dup.treePrototypes = CloneTreePrototypes(original.treePrototypes);
			dup.treeInstances = CloneTreeInstances(original.treeInstances);

			return dup;
		}

		/// <summary>
		/// Deep-copies an array of splat prototype instances
		/// </summary>
		/// <param name="original">Prototypes to clone</param>
		/// <returns>Cloned array</returns>
		static SplatPrototype[] CloneSplatPrototypes(SplatPrototype[] original)
		{
			SplatPrototype[] splatDup = new SplatPrototype[original.Length];

			for (int n = 0; n < splatDup.Length; n++)
			{
				splatDup[n] = new SplatPrototype
				{
					metallic = original[n].metallic,
					normalMap = original[n].normalMap,
					smoothness = original[n].smoothness,
					specular = original[n].specular,
					texture = original[n].texture,
					tileOffset = original[n].tileOffset,
					tileSize = original[n].tileSize
				};
			}

			return splatDup;
		}

		/// <summary>
		/// Deep-copies an array of detail prototype instances
		/// </summary>
		/// <param name="original">Prototypes to clone</param>
		/// <returns>Cloned array</returns>
		static DetailPrototype[] CloneDetailPrototypes(DetailPrototype[] original)
		{
			DetailPrototype[] protoDuplicate = new DetailPrototype[original.Length];

			for (int n = 0; n < original.Length; n++)
			{
				protoDuplicate[n] = new DetailPrototype
				{
					bendFactor = original[n].bendFactor,
					dryColor = original[n].dryColor,
					healthyColor = original[n].healthyColor,
					maxHeight = original[n].maxHeight,
					maxWidth = original[n].maxWidth,
					minHeight = original[n].minHeight,
					minWidth = original[n].minWidth,
					noiseSpread = original[n].noiseSpread,
					prototype = original[n].prototype,
					prototypeTexture = original[n].prototypeTexture,
					renderMode = original[n].renderMode,
					usePrototypeMesh = original[n].usePrototypeMesh,
					useInstancing = original[n].useInstancing,
				};
			}

			return protoDuplicate;
		}

		/// <summary>
		/// Deep-copies an array of tree prototype instances
		/// </summary>
		/// <param name="original">Prototypes to clone</param>
		/// <returns>Cloned array</returns>
		static TreePrototype[] CloneTreePrototypes(TreePrototype[] original)
		{
			TreePrototype[] protoDuplicate = new TreePrototype[original.Length];

			for (int n = 0; n < original.Length; n++)
			{
				protoDuplicate[n] = new TreePrototype
				{
					bendFactor = original[n].bendFactor,
					prefab = original[n].prefab,
				};
			}

			return protoDuplicate;
		}

		/// <summary>
		/// Deep-copies an array of tree instances
		/// </summary>
		/// <param name="original">Trees to clone</param>
		/// <returns>Cloned array</returns>
		static TreeInstance[] CloneTreeInstances(TreeInstance[] original)
		{
			TreeInstance[] treeInst = new TreeInstance[original.Length];

			System.Array.Copy(original, treeInst, original.Length);

			return treeInst;
		}
	}
}

One property is missing while cloning the detail prototypes.
You can add it pretty easily in the line 110.
useInstancing = original[n].useInstancing