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I used to keep all the subs but lately I figured that it's not worth it as I never "restack" them. So once I have done the calibration and saved the RGB masters (as FITS) I delete all the subs, flats, darks and only keep the master fits and the PSD files (that's where all my time goes into). I very often re-open old PSD files. They're all un-collapsed and I keep all the processing steps and name each layer with its blending, % , opacity etc... I finally export a "big" 1:1 version as full quality JPEG then crop and one under 200KB for IIS.
When I backup the data, then I have a list of DSO as main directories and I dump all the masters & PSDs in there as you do but I don't bother keeping track of dates.
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