I might be asking a stupidly obvious question, but if you are selecting the 'Scrap' task instead of 'Refit', can you then find it? You can't scrap a ship using 'Refit'.
It might also be a bug. In the earlier versions, I occasionally experienced that a ship would not show up in the 'Refit from' dropdown menu. If I copied the same ship class, then the copy would show up while the original was missing, so the design was fine for the shipyard. I thought it was fixed if you are on the later versions.