There was a way to have multiple decks for a game. For example, the second can be a double-sided rules card. The game crafter is assuming that I don't want a second deck because the card back was the same as the one already used, so it wasn't letting me add another deck that way. I disagree with this assumption and it caused frustration. I had to add a different card back then change it to be the same.
The new system allows for replacing files in bulk, and in order to allow that, it has to do that by filename. So if you try to upload a file with a filename that already exists, it will assume that you are replacing the existing file.
The simplest solution is to make a copy of the card back on your computer, rename it, and upload it as the back of the second deck.