Pretty sure there is an easier way as I did this once upon a time when I was very new to calibre.
I think I just saved the books with template, dragged them back and converted them to embed changed filename. (with merge duplicates off of course)
Another option is to embed metadata at the start of the book.
Now I just have the standard title etc. and rely on my memory
and the Calibre catalogue.
To organise books on my sony in book view I would have to put author->series->number->title and that looks way ugly