Keep only the four corners of the nine-patch image and combine them into a small image.

ClipNinePatch.cs

using System.IO;
using UnityEngine;
using UnityEditor;

public static class ClipNinePatch
{
    [MenuItem("Assets/Clip Nine Patch", true)]
    static bool ValidateClipNinePatchImage()
    {
        Texture2D texture = Selection.activeObject as Texture2D;
        if (texture == null)
        {
            return false;
        }

        string path = AssetDatabase.GetAssetPath(texture);
        TextureImporter importer = AssetImporter.GetAtPath(path) as TextureImporter;
        if (importer == null || importer.textureType != TextureImporterType.Sprite)
        {
            return false;
        }

        return true;
    }

    [MenuItem("Assets/Clip Nine Patch")]
    static void ClipNinePatchImage()
    {
        Texture2D texture = Selection.activeObject as Texture2D;
        if (texture == null)
        {
            EditorUtility.DisplayDialog("Select Texture", "You must select a texture first!", "OK");
            return;
        }

        string path = AssetDatabase.GetAssetPath(texture);
        TextureImporter importer = AssetImporter.GetAtPath(path) as TextureImporter;
        if (importer == null)
        {
            EditorUtility.DisplayDialog("Import Texture", "Failed to import texture: " + path, "OK");
            return;
        }

        bool originalIsReadable = importer.isReadable;
        if (!originalIsReadable)
        {
            // Make texture readable temporarily
            TextureImporter tmpImporter = AssetImporter.GetAtPath(path) as TextureImporter;
            tmpImporter.isReadable = true;
            AssetDatabase.ImportAsset(path);
            importer = tmpImporter;
        }

        var border = importer.spriteBorder;
        // Calculate new texture size
        // x left z right w top y bottom
        int newWidth = (int) (border.x + border.z);
        if (newWidth == 0)
        {
            newWidth = texture.width;
        }

        int newHeight = (int) (border.w + border.y);
        if (newHeight == 0)
        {
            newHeight = texture.height;
        }

        // Create new texture and fill with transparent pixels
        Texture2D clippedTexture = new Texture2D(newWidth, newHeight, TextureFormat.RGBA32, false);

        // The lower left corner is (0, 0)
        // Copy corner pixels to new texture

        // top left corner
        Color[] cornerPixels;
        if (border.x * border.w > 0)
        {
            cornerPixels = texture.GetPixels(0, (int) (texture.height - border.w), (int) border.x, (int) border.w);
            clippedTexture.SetPixels(0, (int) (newHeight - border.w), (int) border.x, (int) border.w, cornerPixels);
        }

        // top right corner
        if (border.z * border.w > 0)
        {
            cornerPixels = texture.GetPixels((int) (texture.width - border.z), (int) (texture.height - border.w),
                (int) border.z, (int) border.w);
            clippedTexture.SetPixels((int) (newWidth - border.z), (int) (newHeight - border.w), (int) border.z,
                (int) border.w, cornerPixels);
        }

        // bottom left corner
        if (border.x * border.y > 0)
        {
            cornerPixels = texture.GetPixels(0, 0, (int) border.x, (int) border.y);
            clippedTexture.SetPixels(0, 0, (int) border.x, (int) border.y, cornerPixels);
        }

        // bottom right corner
        if (border.z * border.y > 0)
        {
            cornerPixels = texture.GetPixels((int) (texture.width - border.z), 0, (int) border.z, (int) border.y);
            clippedTexture.SetPixels((int) (newWidth - border.z), 0, (int) border.z, (int) border.y, cornerPixels);
        }

        // without top and bottom
        if (border.x + border.y > 0 && border.w + border.y == 0)
        {
            cornerPixels = texture.GetPixels(0, 0, (int) border.x, newHeight);
            clippedTexture.SetPixels(0, 0, (int) border.x, newHeight, cornerPixels);

            cornerPixels = texture.GetPixels((int) (texture.width - border.z), 0, (int) border.z, newHeight);
            clippedTexture.SetPixels((int) (newWidth - border.z), 0, (int) border.z, newHeight, cornerPixels);
        }

        // without left and right
        if (border.x + border.z == 0 && border.w + border.y > 0)
        {
            cornerPixels = texture.GetPixels(0, 0, newWidth, (int) border.y);
            clippedTexture.SetPixels(0, 0, newWidth, (int) border.y, cornerPixels);

            cornerPixels = texture.GetPixels(0, (int) (texture.height - border.w), newWidth, (int) border.w);
            clippedTexture.SetPixels(0, (int) (newHeight - border.w), newWidth, (int) border.w, cornerPixels);
        }

        // Apply changes to new texture and save as a new asset
        clippedTexture.Apply();

        importer.isReadable = originalIsReadable;
        AssetDatabase.ImportAsset(path);

        string defaultPath = Path.GetDirectoryName(path);
        string fileExtension = Path.GetExtension(path)?.Substring(1);
        if (string.IsNullOrEmpty(fileExtension))
        {
            EditorUtility.DisplayDialog("Error", $"Unsupported file extension: {fileExtension}", "OK");
            return;
        }

        string newPath = EditorUtility.SaveFilePanel("Save Clipped Texture", defaultPath,
            $"{texture.name}_clipped.{fileExtension}", fileExtension);
        if (string.IsNullOrEmpty(newPath))
        {
            EditorUtility.DisplayDialog("Error", "Failed to save clipped texture: path is empty", "OK");
            return;
        }

        byte[] bytes;
        switch (fileExtension)
        {
            case "png":
                bytes = clippedTexture.EncodeToPNG();
                break;
            case "jpg":
                bytes = clippedTexture.EncodeToJPG();
                break;
            case "tga":
                bytes = clippedTexture.EncodeToTGA();
                break;
            case "exr":
                bytes = clippedTexture.EncodeToEXR();
                break;
            default:
                EditorUtility.DisplayDialog("Error", $"Unsupported file extension: {fileExtension}", "OK");
                return;
        }

        File.WriteAllBytes(newPath, bytes);
        AssetDatabase.Refresh();
    }
}