I don't think the common conversions were ever bugged since none of them are "iconic" (lore). I tested the Uncommon conversion yesterday. I used one of my 3 copies of Dwigus (spelling?) and an extra copy of Orc Arsonist (it was definitely one of the orcs). Poof...all copies gone on both of them. Definitely not fixed in any way. Personally, I think the game is supposed to prevent you from getting dupes of Unocommon and above agents since they're "lore" and can only do one quest at a time, and the conversion quests are coded to remove that agent, not taking into account duplicates.