You have all the files you need. The en-US is what is inside the final download/extraction.
In other words if I copy past them, it will replace the older files. Should I do that ?
That is actually a good question. For the library, copy away. And for the others, it does not appear to matter. But, for example, with styles, the styles you have in your styles folder now were installed by the .exe that installed some Encore and Premeire Pro styles, templates, etc. In the Encore en-US styles, you will see some with .psdloc extensions, rather than .psd extensions. When you copy those, the ones with .psdloc will not work. But they are all (I think) already in the styles folder. Copying over them will not replace the ones that were previously without the .psdloc. I don't really know how all this works. It still looks like this is a mess.
But put the library where they go, and you will have the content you need.