Insert Date / Time Button (Formating Issue)

You do not describe how you made the modifications so I don't know what might have caused them to not work anymore.
Note however that we don't support any modification of the editor library or the module itself. We now (as of 2.1) have hook_wysiwyg_editor_settings_alter which you can use to customize the settings object sent to TinyMCE (or any other editor) until we have a proper GUI. There's a short example of how to use it in #313497-52: Allow configuration of advanced editor settings.

I'm not sure what you mean by "Then the format could be managed by Tinymce in the insertdatetime - editor_plugin.js the way the editor expects.". The plugin only replaces the %-placeholders in the plugin_insertdate_dateFormat and plugin_insertdate_timeFormat settings with the current date/time values and inserts the new string at the cursor position. The values we use are the same ones given as examples on TinyMCE's wiki: insertdatetime, which are also the default values.

Once we fix #313497: Allow configuration of advanced editor settings (major requirement for Wysiwyg 3.x), we'll have a GUI option to change these settings. Until then, you can implement the new hook to change them to whatever you want without having to hack the module or the editor library:

function myModule_wysiwyg_editor_settings_alter(&$settings, &$context) {
  if ($context['profile']->editor == 'tinymce') {
    $settings['plugin_insertdate_dateFormat'] = '%D';
    $settings['plugin_insertdate_timeFormat'] = '%r';
  }
}