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Hi,
Are you using the command line version, or the GUI?
In the GUI, you can right-click a row in the grid, and choose "Exclude all different" and "Exclude all on left", which should do the trick.
In the command line, have a look at the /ignoredifferent and /ignoremissing options (you can get more details by running SQLDataCompare.exe /help /verbose).
Hope that helps,
Robert
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What is the proper way to handle this?