I upgraded this mod in my existing save that uses Mk3 E-locomotives and discovered that a new setting was added for whether the upgraded locos are available.

However, the new setting defaults to off, which removes the recipes and technologies from existing games (but thankfully leaves the locos themselves alone). The new setting should default to ON, to match the previous behavior before the setting was added.

As a side note, I'd be happy to submit a patch if you have the mod up on GitHub or somewhere. I couldn't find it, but that doesn't mean it isn't up.