I agree with you the author should maintain this but if your tool is deleting the libs and is not making the addon be dependent on it anymore (as direct calls to the lib files in the addon's txt is not creating any dependency in the ingame addon manager) it most likely will just break the addon.
So at least adding/changing an exisitng line and add to the end of would be needed, or your tool got just a 25% chance to make things better (depending on how and when the authors included the libs in their code):