My problem is simple. I pick a certain item in CAS, and everything is fine, but when I go to live mode this item gets replaced with another one (and it's not like CC is getting replaced with base game/EP items, sometimes these items are replaced by other CC). To be more specific, this happened with three custom chokers and one hairstyle (I wouldn't say this is relevant but who knows).
I use nrass's Master Controller mod to disable clothing filter, but I checked with S3PE and these specific items are all categorized correctly.
If there's no way to fix this, I'd at least like to know if there's a reason so that i can avoid it and play with that into account?
Sounds like the CC meshes were only set to Very High Level Detail, but in your Settings your sim detail was only set to Medium, for instance. CAS always shows everything in VHLD, but in Live Mode it'll revert back to your own game settings, and the CC will disappear, being replaced by whatever it was originally cloned from.
So you'll either have to:
1: use other CC
2: contact the CC maker (if they're still active), like Nitromon said
3: if you're familiar with TSRW, fix the CC yourself (could take a few minutes or quite some time, depending)
4: adjust/raise your game settings to Very High Detail (worst case scenario if your PC can't handle it)