Views can be synchronized with Data Compare for MySQL only if they reference rows from a single table.
To synchronize views that reference more than one table:
1. Compare the views with Data Compare. When configuring the comparison options in the New Data Comparison Wizard, make sure that the Compare views checkbox is selected.
2. Notice which rows are different.
3. Use the Data Compare tool to compare and synchronize the tables with the different rows.
You cannot directly synchronize queries with Data Compare. But you can get an update script and apply it against a target database instead.