Rebuild a mysql slave adding innodb_file_per_table without locking the master
really all could be shorter:


Stop mysql on Slave, change settings, Start MySQL on Slave
Login to MySQL; Stop slave; exit from mysql client
make dump from Master direct from Slave:



  mysqldump --host=Master_IP --port=Master_port -u
  user_with_enought_rights -p --single-transaction --all-databases
  --master-data=1 > dump.sql



restore dump on Slave



  mysql -u root -p &lt; dump.sql



start Slave


It will not lock master (in case of InnoDB tables) and automatically adjust Slave to Master position