Couldn't it be possible to orgagnize them by game-mode, and then one game-mode save with "other", which is where you can put builds you're working on, or backup saves.
That sounds like the most difficult to use sorting system ever. Rather than folders, it should just be a categorized "Viewing" system.
View All, View Old (Pre v21), View New (Post v21), View Backups
Maybe even View Default.