You lose the rune the moment you use it, rather it be by mistake, to use the rune's property, to complete a runeword, or in a cube recipe. If you have already made a good runeword, I would keep the item and find another socketed item to make another runeword. If you accidentally used the rune, then it's gone, no matter how accidental it was. One of the things that pretty much suck but there's nothing that can be done about it. Once it's used it's gone, part of something else now.