I've made this to append a query string with a "number version" according to the assets content, so it works as Cache BUST for CDN caching services (i.e: cloudfront). It only check the last modified date of each asset inside a bundle and create a token, you can create a MD5 o change to something more cool. The code is executed wen a file changes…

.net Bundling version with UseCdn = true

    /// <summary>
    /// uses the BuildCundleContent to create a file midification token, but we need to keep the  BaseBuilder functionality, so we 
    /// take them from the ctr.
    /// </summary>
    public class SetAssetVersion : IBundleBuilder
    {
        public IBundleBuilder BaseBuilder { get; set; }

        public SetAssetVersion(IBundleBuilder baseBuilder)
        {
            BaseBuilder = baseBuilder;
        }

        public string BuildBundleContent(Bundle bundle, BundleContext context, System.Collections.Generic.IEnumerable<BundleFile> files)
        {
            if (bundle == null)
            {
                throw new ArgumentNullException("bundle");
            }

            long tokenTime = 0;

            foreach (BundleFile file in files)
            {
                if (HttpContext.Current != null)
                {
                    var fileInfo    = new System.IO.FileInfo(HttpContext.Current.Server.MapPath(file.VirtualFile.VirtualPath));
                    tokenTime       += fileInfo.LastWriteTimeUtc.Ticks;
                }
            }

            bundle.CdnPath = bundle.CdnPath.Split(new char[] { '?' }, 2, StringSplitOptions.RemoveEmptyEntries).First()
                                    + "?v=" + tokenTime.ToString();
            
            //return the original result of the BuildBundleContent method from the BaseBuilder (Default).
            return BaseBuilder.BuildBundleContent(bundle, context, files);
        }
    }

Bundle configuration

public static void RegisterBundles(BundleCollection bundles)
{
    BundleTable.EnableOptimizations = true;
    bundles.UseCdn = true;

    StyleBundle cssBundle = new StyleBundle("~/bundles/css", 
                                            "http://cdn.localhost:39061/bundles/css");
    //using our coustom code, and keeping the base builder
    cssBundle.Builder = new SetAssetVersion(cssBundle.Builder);
    
    cssBundle.Include("~/css/Copy of miceceese.css",
                         "~/css/miceceese.css",
                         "~/css/periplo.css");

    bundles.Add(cssBundle);
    
    //result: http://cdn.localhost:39061/bundles/css?v=6352530398450671462
}