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Yes, you can use the Copy To Folder command to copy any selection to a 3rd location. Set your display filters to show only the files you wish to copy (Show Differences), issue an Expand All command (Edit menu), and a Select All Files command (Edit menu), then use Shift+Arrow Keys to select just the left or right side. You should now be selecting just the different files on one side, and ready to Copy To Folder.
Thanks! Can I do this through the command line? Ultimately what I want to do is backup some daily data (just the differences) to a new folder that gets created with today's date.
Yes, you can automate it using Beyond Compare's built-in scripting support. See the "Using Beyond Compare > Automating with Scripts" topic in the help file for details. Here's a link to the online version of the help: http://www.scootersoftware.com/help/..._overview.html
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