With myISAM - fine, just restore the files from the backup. With innoDB - sure, you could restore the InnoDB files, but you'd loose any changes in any other innoDB files made since the backup was done.
I guess the only alternative is to do a dump of the InnoDB data before each backup, but that's hardly ideal.
Unless you turn on the option that creates an InnoDB file per table, but that's a bit like overkill. What would be better is an option to create an InnoDB file per database.
grrr. Fortunately nothing was deleted other than an empty XF install, but that's beside the point.