They essentially just don't copy over from the windows.old. I've noticed several repercussions of this. The links get removed from Start, K-lite codecs all broke, context menu items don't re-register; I'm sure there are more. Thankfully appdata and such seems to copy fine.
I'm getting so frustrated with all the problems in every single update, major and minor. Cortana still doesn't work properly for me, and now the Insider app doesn't function. I love windows 10, but it still feels like I'm using an early tech preview.