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MySQL 5.5 Reference Manual  /  ...  /  Replication and REPAIR TABLE Replication and REPAIR TABLE

When used on a corrupted or otherwise damaged table, it is possible for the REPAIR TABLE statement to delete rows that cannot be recovered. However, any such modifications of table data performed by this statement are not replicated, which can cause master and slave to lose synchronization. For this reason, in the event that a table on the master becomes damaged and you use REPAIR TABLE to repair it, you should first stop replication (if it is still running) before using REPAIR TABLE, then afterward compare the master's and slave's copies of the table and be prepared to correct any discrepancies manually, before restarting replication.

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