Ah yes, the fly box cleaning/organizing process ..... not an easy task my friend !!
Like you, I have been through this excercise in an attempt to simplify my boxes and reduce the amount of choices on the river. Scattered patterns are difficult to sort through on the river, which makes for lost time in actual fishing. What's worse is the lack of confidence in your chosen offering sometimes.
I like your thought process, organizing your boxes into seasons or river conditions, I do the same now. This way I'm not carrying all my wallets which only loads me down and sorting through every fly.
I will add to your dilemma by adding the variable of river conditions for your thought process while attempting to fill your boxes
In the long run, it will only help you. No sense bringing a 4" heavy dressed shank to the river when the river has low flows.
Late summer and early fall time river conditions in my area are low, so I stick with sparsely dressed hairwings, quill wings and mixed wings. I reduce the patterns and tie on low water style hooks. This helps the fly sink on it's own and eliminates the use of tips or at least use light tips.
My go to patterns for this time:
Green Butt Skunk
Thunder & Lightning
Hope that helps