After programmatically modifying enterprisehomescreen.xml, try calling the "home" screen intent. This should force EHS to reread it's config xml.

Intent startMain = new Intent(Intent.ACTION_MAIN);
startMain.addCategory(Intent.CATEGORY_HOME);
startMain.setFlags(Intent.FLAG_ACTIVITY_NEW_TASK);
startActivity(startMain);

You could also copy a file that exists in the devices file system to enterprisehomescreen.xml, then call the homescreen intent.

Add this to a method, or button call back:
        InputStream in = null;
        OutputStream out = null;
        try {
            //in = assetManager.open(filename);
           in = new FileInputStream("/enterprise/usr/enterprisehomescreen_new.xml");
            out = new FileOutputStream("/enterprise/usr/enterprisehomescreen.xml");
            copyFile(in, out);
            in.close();
            in = null;
            out.flush();
            out.close();
            out = null;

            Intent startMain = new Intent(Intent.ACTION_MAIN);
            startMain.addCategory(Intent.CATEGORY_HOME);
            startMain.setFlags(Intent.FLAG_ACTIVITY_NEW_TASK);
            startActivity(startMain);

        } catch (Exception e) {
            Log.d(this.getPackageName().toString(), e.getMessage());
        }

Add this method in your class:
private void copyFile(InputStream in, OutputStream out) throws IOException {
        byte[] buffer = new byte[1024];
        int read;
        while ((read = in.read(buffer)) != -1) {
            out.write(buffer, 0, read);
        }
    }