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I think you can batch-extract files in S4PE, and I think files with pictures in them save as DDS, but I'm not sure. I think it's possible to extract textures as DDS, so it would just be a matter of replacing them.
There's a batch-tool in Photoshop that can either run one particular task, or an action set. I've often used it to convert RAW camera files to JPG or some such. Just open on of the files and make an action that does what you want. Then you put all the files you want to convert into a folder, find the batch tool, and set it to run the action on the files in that folder. No idea if the RLE2 files can be opened with Photoshop, though. You may need a DDS plugin, too.