I have the strong feeling it's an e-shop server related problem. An installed .cia game update also registers you at the Nintendo servers as 'downloaded the game update'. But it somehow knows it's
not exactly the same as their game updates. A perfectly made .cia update would never cause this whole problem.
So no wonder it tries to 'redownload' in e-shop when you haven't even downloaded the update in the first place.
That official 'redownload' cannot continue since you never got it from the eshop to begin with and that's causing the whole 99% downloading error!
So that's why a second Emunand is needed to get you the status of legitimate first time downloader at the Nintendo e-shop servers.
After that... The e-shop is tricked in believing that I made a legitimate first download and I can just swap in my original Emunand and the
downloads work.
So like you said.. It's an e-shop server registering problem which seems very logical right now.