The times I have lost images have been my own fumble-fingers after my initial download. I shoot RAW+JPG, download to my computer SSD drive WITHOUT deleting them from the SDHC card. Then, once on my SSD, I make my 'first cut', viewing each JPG with Windows Photo Viewer, and simply delete both the RAW and JPG if it isn't, at first glance, a keeper. On occassion, I find my moving 'fast' has resulted in the wrong RAW being deleted. Typically, I don't discover this until sometime during 2nd or 3rd processing cycle when I think: "where's that photo of...".
As fjrabon above indicated, not deleting the images from the card until ALL selection and processing is completed has saved me every time. Now my only problem is remembering to format the card before I use it for another shoot.
It should also be noted that my workflow produces 4 distinct folders, each with a full 'set' of processed pictures, the output of every step. That way, if I need to back up 1 step, or 2 steps, or whatever, I still have it. I copy daily all 'current, in process' shoots to a 16gb thumb drive I keep in my pocket until everything is 100% put to bed.