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This should not a problem, provided you do not execute any DDL related to the Storage Engine on the Master. I have written about this many times Jun 01, 2011 : What can we do in MySQL 5.0 Replication to address bandwidth concerns? Nov 16, 2011 : Log MySQL DB changing queries and users Mar 13, 2012 : http://dba.stackexchange.com/questions/14943/setting-up-...
UPDATE `GLOBAL_VARIABLES` SET `VARIABLE_VALUE`="InnoDB" WHERE `VARIABLE_NAME`="DEFAULT_STORAGE_ENGINE"
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