Converting from InnoDB tables to innodb_file_per_table
The process you mentioned works fine but it takes much amount of time if the tables are bigger  in size 
Here the way you can do it quickly .but it requires some down time depends on the table size .


Take the full backup of 20 tables that are InnoDB.
Drop those 20  tables that are InnoDB
Stop mysql 
Delete the ibdata files
Start the mysql services with  innodb_file_per_table=1 in my.cnf
Restore those 20  tables that are InnoDB with taken backup.