Re: Removing schema information from MySQL system files
Okay, apparently the bytes are not overwritten, though the data is now inaccessible through SQL queries. The space that used to be occupied by those rows is now marked as free, and subsequent activity on those tables may reuse the space.
If you've uninstalled MySQL Server, and your application was the only user of MySQL Server, feel free to delete those files too.
It's customary for uninstallers to not remove files that have been modified since installation, such as databases, config files, log files. You can delete these files after installation if you choose, and you must do it explicitly; the uninstaller won't (and shouldn't) do it.
If you need to leave a functioning MySQL Server in place, you could back up & restore the 'mysql' privileges database. That should recreate the tables fresh, without the "ghost" data in the free space within the file.
You can also try "ALTER TABLE db ENGINE=MyISAM" which may restructure the table, creating the file fresh, containing only current data and no "ghosts".
Regards,
Bill K.