I've run into the following scenario: we've got several database servers with 2+TB of data spread across several 900GB InnoDB data files. We can move to innodb_file_per_table in an incremental fashion (ie ALTER TABLE ENGINE='InnoDB' one table at a time), however, to complete this task, we'll need to phase out the existing ibdata files and delete them. Is there a way to safely delete ibdata files after the data has been removed from them without doing a mysqldump and re-import? Unfortunately we can't take the databases down for the multiple days it would take to do a full mysqldump based migration.
Thanks, -Aaron
