I do similar to what has been mentioned. Before I "accept" a trade, I go to my traders and verify that I have the pin and that it is in good condition. When I have received the other trader's address I print off a record of the trade, go get the pin, and remove it from my trade list. I don't remove pins from my wants list until I physically have the pin in hand. Unfortunately, things happen and the pin never comes. I will update my Pinpics when I am unwrapping the pin. With it still on my wants list, it makes it easier to find, since my wants list is manageable.
But I also recently audited my pin collection. I have a large collection 5000+ pins, so it took most of a month to do. When I was done, I had over 100 pins that weren't on my owns list, and I found a dozen or so pins that I have never owned on my list. And another dozen or so pins that I had owned at one time, but decided to trade, probably traded at an Epcot pin event and never removed from my owns list. If you look at the URL of a Pinpics trade, sometimes you will notice an act=atw, act=adw, etc at the end of the URL. This is the the part that adds or removes the item from your list. Sometimes, people grab that URL to put in a post and when you click on it, it will add or delete from YOUR lists. So this makes it looks like "gremlins" got on your list and messed it up.
And unfortunately, I too, ended up with one pin that I can't find for the life of me. I don't know if I assumed I had it when I got the rest of the set, or if I've just lost it somewhere. Unfortunately, I don't think it will be that easy to replace, because there are a lot of C&D collectors who want it too.