My brain hurts too and I am a Nikon user.

My routine, for what it is worth is not to use Nikon's software at all - I find it clunky and difficult. I stick the SD card into the computer, open it and plonk all the images into a file labeled "today's download" in my "camera images" file. I them eject the card and set it aside without deleting anything except, perhaps, a few hopeless pics.

Any post work I do on the copies in the computer before placing the keepers into their various files for permanent storage. Only when I have finished all my fiddling and the new images have been uploaded to Dropbox do I put the card back into the camera and format it. That way if I (usually) or the computer stuffs up the image is not lost.

Don't ask how I learned to do it this way- it is embarrassing.