I'm using Lightroom to straighten tilted horizons automatically. I care about straight horizons, but I don't care about image quality, so I shoot jpg and want to override my files. Lightroom is forcing you to use a certain workflow and you just have to accept this if you want to use it. That's just part of the deal. No need to fight it, just go with the flow. That's what I do: Lightroom - export the changed images: Export dialog: Rename to "Filename - Sequence". Start sequence with 1. Windows Explorer: Sort the images by filename. Then delete every second image. These should be all images that don't end with a 1. Or use a tool like Fast Picture Viewer and mark every image with a tilted horizon for deletion. This gives you a way to quickly delete all original images.
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