Don't mess with the files in the Calibre library directory!
Treat it as a black box.
You
can export them elsewhere (and then delete them from the library if you don't want to keep them there). Preferences > Saving books to disk lets you change the path.
You'll want to go to Preferences > Add your own columns and set up a 'column built from other columns' using
{identifiers:select(isbn)} for use in the save template.
Try out something like
{title}_{author_sort}_{#isbn} after setting up the column -- I'm not entirely sure how to extract just the last name so hopefully someone else will chime in
https://manual.calibre-ebook.com/template_lang.html gives a good overview of everything.