I only do conversions when I have doubles (in agents). Just did an "Uncommon Conversion". For one of the agents I had 2 of them. For the other two I had 3 (one was Equestrielle). Of course you can only select the same agent just once in a slot (would help - even for other quests if there was an error message WHY you cannot start the quest if you have one of those agents assigned twice. At least I couldn't find a message so far.) and start the quest. I was quite puzzled once I found out that ALL instances of these three agents were lost. So instead of just losing 3 uncommon agents I lost the full total of 8. Doing the same with "Common Conversion" it only removes the agents selected and leaves doubles intact.