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Hi Jason,
Can you try the same thing with the 'include dependent objects' turned off? This may be scripted as part of a dependency.
Note: in the next version you'll be able to tell which objects were ones you'd explicitly chosen and which are dependencies. Good news there! -
Oh, by next version I don't mean 4, which is already out. I mean version 5.
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If you check the following image, you can see that, although I have unselected the "orders" table, the code in the script drops columns from this table.
The version of SQL Compare I am running is 3.2.1.14
Thanks,
Jason