I also keep all of the NEFs, but with long focus stacks, that can be 100 or more layers and with pixel-shift in the new Pentax K1, the file size is like 150 MB for each layer, so it adds up. At the same time, I want to preserve my finished TIFF files, since in my recent health crises, it was very clear to me that there will come a time, and not that long, when someone else has to deal with the many hundreds of thousands of images that I have. Not many want to do that, so I would like to save the finished TIFFs in the best color space, ProPhoto RGB, so that at least the finished pieces could be utilizes, so that is what is bringing this consideration on.
Once I create a stack, I save the layered stack as
Master TIF file, and then I delete
all of the raw images that comprised it (as the raw images only take up space and are useless individually).
I save the un-edited Master Tiff in the ProPhoto Color Space, in a special section of folders I create in my Photography directories (say a "Flower" folder, or folder to which the Master Image applies)
I *only* edit the Master TIF
in layers (so I can un-do anything I don't like, later, even after saving, as layered TIFs can be un-layered ... whereas, if you edit/save and compress the layers, you can never un-do what you've done).
In fact, usually, I save any edits I've made as separate TIFs (e.g., Flower1.tif , Flower2.tif), always keeping my Master Tif clean and pure as-rendered from the original stack.