I'm using 3.0-BETA3 and I could swear it didn't do that before, but it's now DELETING the original DNG files, leaving only a -dualiso.DNG file present, much to the surprise of my Lightroom. I think it started happening when I set LR to convert files to DNG, whereas I had it set to import my CR2 files without converting. I'm not sure if it's cr2hdr or the plugin that's responsible; I'll make sure by running cr2hdr in command-line mode, if needed.
Also, it doesn't copy the original camera metadata into the dualiso file; rather, it sets my f-stop and exposure time both at 1, what's with that? It was just an annoyance before, as I could always look up these tidbits on the original files, but now that cr2hdr (or the plugin?) deletes my original files, I can't look at the exposure data anymore.