Honestly, I don't know everything ;-)
I also tried to prevent drops of certain ingredients I wanted to replace, because crafting recipes can not be disabled.
So first, I changed the treasure classes of the 'disabled' items in the link file to something like '..._DISABLED', expecting those items no longer to drop. It did work, but only partially. In one test, I found an item that should not have dropped in a crate. So I knew it would not work that way.
It seems like we cannot override the links completely, but what seems to be kinda safe is TreasureTable.txt.
Then I changed the treasure classes of the items I wanted to keep instead of those I wanted to get rid of and changed TreasureTable.txt accordingly. (Of course I removed or replaced the deprecated items if they were in TreasureTable.txt directly as "I_...".)
So no matter if the original treasure class 'leaks through', those items no longer drop because TreasureTable.txt seems to work all the time and not half the time only, or if you're lucky, like many other systems.
... at least I did no longer receive any old items in my one playthrough with XC_Bags.
And I don't remember any reports of users that they received unexpected items.
Unfortunately, with Divinity, this still says nothing, I might have been lucky and other players might have only shrugged their shoulders instead of posting anything.
But it might be worth a try.
You know that I don't have real knowledge but a lot of speculation, and my speculation on this is, that links cannot be fully overridden but are somehow merged, like crafting recipes almost, and I think, the reason might again be that stupid MainLSF.pak nonsense. (... speculation though, not knowledge!! ;-)
Hope this helps. If you need examples just compare the link files in XC_Bags with the originals from Main.pak, especially Object.txt.
D:OS EE is a buggy mess and modding unfriendly as hell, and has zero official support except from poor Raze.
That's the reason why my motivation for EE modding has drastically decreased and my interest and motivation for D:OS2 is below zero currently.
(I'm of course still interested in technical aspects - not really of version 2 - and will help as much as I can, because it's not the fellow modders' nor players' - nor Raze's - fault. But as said, my knowledge is finite like everybody else's ;-)
Having all that said I have to give you two guys + Abraxas my biggest respect because you guys are still fighting with this nasty beast ;-)