.../data/
will have the same number of subdirectories -- because you have not dropped any databases.
.../data/foo/
will have a .frm file for each table in the database `foo`. It should not have any .ibd files, if the conversion worked as planned.
You did do
SET innodb_file_per_table = OFF;
USE foo
ALTER TABLE table1 ENGINE=InnoDB;
ALTER TABLE table2 ENGINE=InnoDB;
...
?
And you still see a file named .../data/foo/table1.ibd ?
If so, I must be wrong about that flavor of ALTER TABLE in the version of 5.6 that you are running. Which version is it? (I am looking for the xx in "5.6.xx".)
Is the .ibd file empty (zero-length)? If so, I see this was fixed in 5.6.9, which might be relevant:
" After issuing ALTER TABLE ... DISCARD TABLESPACE, an online DDL operation for the same table could fail on Windows systems with an error: Got error 11 from storage engine. An ALTER TABLE (
http://dev.mysql.com/doc/refman/5.6/en/alter-table.html ) statement with the ALGORITHM=INPLACE clause could also create an empty .ibd file (
http://dev.mysql.com/doc/refman/5.6/en/glossary.html#glos_ibd_file ), making the tablespace no longer discarded. (Bug #14735917) "