if you sync the notes, you will sync with the notes application inside the calendar application. This is not the same as the default notes application programs menu. But that could be a way of syncing the notes.

If you copy the .txt notes to the MyDocs directory you can probably open the notes in the default notes application too.

You could also try to reformat the notes to the format used by the n900 notes application, it is a simple xml structure, that a small python script could easily do. That way you would keep any formatting.

You could also try an alternative notes/text-editor/wiki program like Conboy, leafpad or Zim.