Further to sn123py's remarks -
I've been using lrf2lrs quite a lot recently in order to edit some lrf files that have typos or bad formatting. Then I use lrs2lrf to get it back onto the reader. Unfortunately, my lrf files are also created from BookDesigner, so I too noticed that the headers and footers get dropped. This is quite annoying since the books look so much better with the header and footers.
Are there any plans to modify lrs2lrf so that it will support the headers and footers? Or is there a better way to edit lrf files without loosing these elements?