I finally committed to sacrificing all my duplicate Runes today, and one of them really gave me a lot of trouble: I had 3 Griefbearer's Fountains, and it said all three were in use. Cue replacing every single one, one-by-one, in every deck, and it still gave me the error. I tried refreshing the Rune Forge, nothing. Looked through every deck—which took a while—nothing. Finally tried taking out all copies and navigating away from the deck, letting it finalize, then going back and readding it. At no time did I choose the third of three copies. It looks like—and I just tested this a few times—whenever you add a rune, say the second of two, remove the rune, then add the first of that rune, it just puts the one you removed back in. I took a set of five Bloated Toads, first had 23 Exp, second had 2, third, fourth and fifth had 0. Added second and third. Refreshed. Verified the one I was removing was the second (2 Exp), took it out, added the first. Immediately checked the two in the deck, were still the second and third. Refreshed, navigated away, everything, still the second and third. As a suggestion in addition to this, ideally, there would be some way that this could be improved so that you can take out all the erroneously-placed duplicates from years ago, in your list of 150+ decks, so that you can more easily utilize the Rune Forge, or even trade copies with some experience to other players.
