Further proof:
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After installing new textures to global4_chr.s3d, it recognized and selectively patched only those textures, while skipping through the rest of the S3Ds. So basically, no matter how many times you run patch_s3d_textures.bat, it will never patch and then repatch the same texture twice.
In light of this I've gone ahead and replaced the .old purge in the batch file.