How to safe delete (shred) a MySQL database?
InnoDB leaves user data in several places.


ibdata1 if innodb_file_per_table=OFF or respective *.ibd file if innodb_file_per_table=ON. This is where InnoDB stores the data.
ib_logfile0 and ib_logfile1 stores recent modifications.
Double write buffer (which resides in ibdata1 no matter what innodb_file_per_table is) stores recent modifications.


To reliably delete user data you need to shred ibdata1 - because of the double write buffer. If you do that, MySQL instance will be destroyed. So, I would say it's impossible to "shred" a particular database/table.

In your case I would create a replica with mysqldump (or mydumper, not with xtrabackup or a file system snapshot) and destroy the original instance/disk/server.