Download and install Sandboxie (http://www.sandboxie.com) and use this Editor script to open up another instance of your Unity project.

Sandboxie.cs

using System;
using UnityEditor;
using System.Diagnostics;

public class Sandboxie
{

	[MenuItem("Sandboxie/Open Sandboxie instance")]
	public static void OpenSandboxieInstance()
	{
		var process = new Process();
		process.StartInfo.FileName = @"C:\Program Files\Sandboxie\Start.exe";
		process.StartInfo.Arguments = EditorApplication.applicationPath + " -projectPath \"" + Environment.CurrentDirectory.Replace("/", @"\") + '"';
		process.Start();
	}

}