Batch image program to replace 2 colors?
For a single color replacement I suggest you use XnView's batch processing tool:
If you need to replace a range of colors, or use tolerance settings (especially useful for JPEG images where neighboring pixels might have slightly different colors - sometimes imperceptible to the eye), I recommend Batch Images. It's also more user friendly for batch processing:
Disclaimer: I am a frequent user of both XnView and Batch Images.