Eco supports making partial overrides and extensions to the base .cs files.
These mods shouldn't override the whole base files anymore as it creates these types of issues where unrelated aspects of modded items override each other.
Not much help for users, but hopefully modders will switch to doing this instead over time :)
Edit: Shouldn't server owners just be able to apply the existing mod versions though? It may overwrite changes in this update, but it should still work 🤔