PBXProject.RemoveFileFromBuild

Удаляет указанный файл из списка файлов для сборки для указанного объекта.

using UnityEditor;
using System.IO;
using UnityEditor.Callbacks;
using UnityEditor.iOS.Xcode;

public class Sample_RemoveFileFromBuild  
{
    [PostProcessBuild]
    public static void OnPostprocessBuild(BuildTarget buildTarget, string pathToBuiltProject)
    {

        // Stop processing if build target is not iOS
        if (buildTarget != BuildTarget.iOS)
            return;

        // Initialize PBXProject
        string projectPath = PBXProject.GetPBXProjectPath(pathToBuiltProject);
        PBXProject pbxProject = new PBXProject();
        pbxProject.ReadFromFile(projectPath);

        // Get the GUID for the Main target
        string mainTargetGuid = pbxProject.GetUnityMainTargetGuid();

        // Get the file GUID you want to remove
        string filePath = "Path/To/ExampleFile.txt";
        string fileGuid = pbxProject.FindFileGuidByProjectPath(filePath);

        // Remove the file from build. Note that this doesn't remove the file from project
        pbxProject.RemoveFileFromBuild(mainTargetGuid, fileGuid);

        // Apply changes to the pbxproj file
        pbxProject.WriteToFile(projectPath);
    }
}