There was a bug report in bugzilla about this and apparently the problem has been resolved with the latest image. see https://maemo.org/bugzilla/show_bug.cgi?id=306

I looked into the backup files just now and the .gpe directory is indeed within the documents.zip file. So it is in the back up. I haven't tried to restore it yet, but it's there it can always be extracted manually when needed.