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There shouldn't be any correlation between files in your Data folder and game recognizing new ones. Sounds like some entry is off. Deleting existing files may solve that.
However, I suspect that you might have to validate game files after deleting those files. This isn't a common problem, so either game or Steam is not detecting some path.
Removing scripted mod from ongoing game borks the game with or without mod manager.
Mod managers indeed make it easier to install and uninstall files, but that does not help you to protect save integrity from script data removal.
Reason for this is that it is not the game itself that stores the script data, but save files. When data is baked in to save file, then removing the script source for it will cause errors in Papyrus VM and eventually break the character.
I want to underline that it does not matter how scripts were introduced - as loose files or archived forms. Outcome is the same, if they are removed from ongoing game.