The config option where you append :false to a line in order to keep traits already existing does not appear to work properly. For example, i have the ice and fire mod installed, and by default, dragonbone handles have the trait fractured II. When i add this line to my tweaker's construct config
dragonbone:handle:jagged,lightweight:false
I expect the dragonbone handle to have fractured II, jagged, and lightweight, however, what actually happens is that the fractured ii trait is removed, and only jagged and lightweight get placed on it.

this also occurs with TAIGA mod's nihilite, where it has the trait soul eater, and i try the following config line:
nihilite:head:xu_xp_boost:false
I expect the nihilite head to have soul eater and experience boost but only get experience boost.

From what I can tell so far it seems like some mods register their materials during pre initialization or post initialization, which doesn't seems to work so well with my mod. I'll see if I can account for that.

I just now realized that there is another issue: when you edit the trait of any material, even just on a single part, it erases all the traits on all the parts of that material that are stock. For example, if i edit dragonbone:head:jagged

Then despite editing only the head part, all other dragonbone parts get their traits erased.
in addition to this, i can't simply put :false into every single other part, because if even one part is missing the false modifier, it will erase all the other part's traits again. This means i am forced to put :false into every single part, but then i am forced to keep all the prior traits on every single part as well.

That's working as intended but I can see why it would be more convenient if it worked the way you described, I'll try to make it work like that.
Meanwhile I have no idea what's causing the original issue, even when the removal of traits is completely disabled, traits are still dissapearing when a new trait is added.