Some CC Missing in CAS (When Filed in Certain Folders)

Hi! I'm working on organizing my CAS CC via Mod Manager (sorting) and S4Studio (CAS Values/DisplayIndex). I organize by creator --> category --> sub-category --> attributes (like short skirts --> denim skirts etc.) 

**The Problem** While checking the in-game catalog, I noticed that skirts from a particular nested folder were missing. They were still missing after I re-did their display indexes, but did show up after I removed all of my mods and tested the missing folders/CC alone. 

**Current Workaround** I ended up moving the folders containing "missing" CC out of order and up a bit in the nest-chain, which did work! 

**My Question** I'm mostly just wondering why this might have happened so I can avoid or fix it in the future. The CC itself doesn't seem to be broken, so I guess it's the folders...Is that possible?

Either way, it's not a huge deal -- the CC's working and I know that I'm playing with fire by messing with the files so much (Especially now that I'm using the new Display Index batch-fix in S4S :D )  -- I just like to organize stuff in a very granular way, and want to understand more about how all of this works! Tysm in advance for your thoughts<3<3