Well, it's official. On all 3 devices, I have to re download books on my Kobo app. On my iPad mini, I deleted the app and redownloaded the entire library. I am in the process of doing the same thing on my iPad 2 right now. I only have a couple of books loaded onto the iPhone, and I have to redo the download to get them to open.
Kobo responded within minutes when I sent feedback via the app. I am still unable to open one book, it stays stuck on "loading" on 2 devices, and I use another app to read it now.
I guess I'm still looking for the perfect epub app for my apple products.