God, working with the CK can be fustrating. I'm trying to make a patched version of a mod so to make sure it'll play nice with another mod (the Siege Bow mod and the ACE Archery component). The ACE longbow/shortbow relationship seems to revolve around the TraitPowerHungry and TraitGreedy keywords, so adding those to the relevant new ammo was the obvious course of action. It seemed to work fine... until I tried reloading the new plugin in the CK to make some adjustments, at which point it started complaining that the necessary keywords didn't exist, and sure enough, any reference to them has totally disappeared. Presumably this is because the game doesn't consider the ACE plugin to be a master of the SBC, even though the latter clearly contains elements of the former. The only way I can think of fixing it is by creating another copy of the original plugin and doing it all over again in one shot, or just not touching the plugin with the CS at all.
It'd be much easier for everyone involved if Bethsoft actually allowed people to make plugins parents of other plugins. Right now it seems to be that if you try to create a "patch" constituted of other mods you'll just end up duping everything you edit but lose everything you don't, and if you make an entirely new plugin you can't inherit elements from others, regardless of load order (because the CK apparently doesn't respect that and deletes the bad entries, even if you actually do have everything loaded).
It might be worth noting that this entire problem stems from the hex-ID system that was put in for Oblivion, which I expect is just as unpopular now as it was then. Morrowind did have engine problems when it came to ID resolving, but those bugs were totally fixable without turning "everything has a unique ID, if IDs conflict the one loaded later overwrites the earlier one" into "everything is tied to a mostly arbitary hex code that's also tied to your load order so it's different for every user and you can have different objects with the same ID in the object ID system which we kept anyway even though we replaced it".