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Is SQLyog (any version) able to synchronize two databases where a table's primary key is an integer with auto_increment?
Data Synchronization Tool is only available with SQLyog Enterprise. Using Data Synchronization Tool you can sync two databases where a table's primary key is an integer with auto_increment.
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Particularly important since the primary keys could be “off” between two copies of a table.
I am not sure if I understood your problem correctly. Please explain the problem with more details.