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What's the easiest way to view differences between two different sets of Gerber files?

Try using Compare jobs, for a quick way to view differences.
  1. Load ALL old gerber to one Job.  
  2. Create a new job (menu: File | New | Job...), and then import the new Gerber files into that job.  
  3. Go to Compare Jobs (menu: Tools | Compare | Compare Jobs) and uncheck "Perform Physical Comparison".
  4. Choose Red (for active job-new), and Blue for Superimposed Job.
  5. Choose either Blend (default) or XOR display.

Then you're able to see all layers using the colors you prefer overlapping each other.

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