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Hello,
I'm afraid that you're right. SQL Compare can compare all triggers or ignore all triggers only. In the current version, triggers are not treated as objects in their own right, but a property of a table. That means you cannot exclude them using the object type filters and you cannot select or deselect individual triggers.
For the time being your best course of action is to save the script and hack out the trigger definitions that you do not want manualy.
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Is this a feature that is a part of SqlCompare or is it that I may have just messed up the syntax?