My routine is that I copy the CR2 files from my camera into their separate folder on my desktop.
From there, I open that folder's contents in Photoshop CS6 which prompts Camera Raw 7.3. Once I edit all my photos and the photos that I do not want, I "delete" them from Camera Raw (places a small red X in the thumbnail). Then when I go to save all and convert the CR2 files into JPGs, separate folder, the photos marked with the red 'X' get automatically deleted, which happen to be the CR2 files.
Any idea how to stop this? For some reason, this did not happen in the previous Camera Raw version... am I missing a preference somewhere?
Yes, this is as designed. Once you choose to delete the file from the camera raw dialog, it will automatically delete it from disk. Thanks.