No internal code to do this, but here is a script to automate Acrobat Professional to do it.
var objShell = new ActiveXObject("shell.application");
var objFolder;
objFolder = objShell.BrowseForFolder(0, "Select the destination folder", 0x10, 0x11);
if (objFolder != null) {
    var DestFolder = objFolder.self.path;
    var fso = new ActiveXObject("Scripting.FileSystemObject");
    var app = pdfe.CreateObject("AcroExch.App");
    var baseDoc = pdfe.CreateObject("AcroExch.PDDoc");
    var ProgressBar = pdfe.ProgressBar;
    ProgressBar.max = pdfe.SelectedFiles.Count;
    for (var i = 0; i < pdfe.SelectedFiles.Count; i++) {
        try {
            FullPathFilename = pdfe.SelectedFiles(i).Filename;
            var Filename = FullPathFilename.substr(FullPathFilename.lastIndexOf('\\') + 1);
            var DestFullPathFilename = fso.BuildPath(DestFolder, Filename);
            if (FullPathFilename == DestFullPathFilename) {
                DestFullPathFilename = FullPathFilename.substr(0, FullPathFilename.lastIndexOf('.') - 1) + '_flattened.pdf';
            }
            pdfe.echo('Flattening: ' + FullPathFilename);
            ProgressBar.position = i + 1;
            baseDoc.Open(FullPathFilename);
            try {
                var JSObject = baseDoc.getJSObject();
                JSObject.addScript("flatten", "function flatten(){this.flattenPages();}flatten();");
                JSObject.removeScript("flatten");
                baseDoc.Save(1, DestFullPathFilename);
                pdfe.echo(" [OK]", 0, 1);
            } catch (err) {
                pdfe.echo(err, 0xFF0000);
                pdfe.echo("");
            }
            baseDoc.close();
        } catch (err) {
            pdfe.echo(err, 0xFF0000);
            pdfe.echo("");
        }
    }
    app.Exit();
    pdfe.echo('\nDone');
}