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With SQLyog Enterprise you can use Notifications Services to execute SQL with the SJA. You can build a batch file with more SJA-instances as explained here: http://www.webyog.com/faq/27_35_en.html . Each instance of course can connect to different servers.
The batch file can be scheduled with the built-in or a third-party scheduler
The .SQL files(s) is/are not executable(s) themselves and can't be scheduled!