You have been told (guilty as charged), that the only way to get rid of the huge InnoDB tablespace file (commonly named ibdata1), when moving to innodb_file_per_table, is to do a logical dump of your data, completely erase everything, then import the dump.
To quickly reiterate, you can only delete the ibdata1 file when no InnoDB tables exist. Delete this file with an existing InnoDB table, even a table in its own tablespace, and nothing ever works anymore.
The problem with the dump-based solution
The impact of doing a logical dump is often overwhelming. Well, the dump may be tolerable, but the restore is much longer. The real pain is that you can't do …[Read more]