OK i think i found what is most probably the core of all the problems we are having with mod lists and mod dependencies;

Mod Manager, upon making the local copy of a mod from the "workshop/content/" directory, adds text to the packageId of the mod in question.
The text added is "_Copy", "Copy1", etc...

In other words, Mod manager edits and changes packageId of any mod it creates the local copy of, not only making mods unable to interact with each other (as they do so via calling on the other mod's packageId), but this action also makes the Mod Manager itself unable to figure out that the copied mods are on a saved modlist as it does not recognize the new, changed packageIds it created.
It's a total, catastrophic mess.

I am just in the middle of manually renaming packageIds of 417 mods by hand. It is a mentally draining process.

I will make a wild guess that you wanted to add "_Copy" to copied mod's directory name instead, but something went wrong.