With this 3 versions my Ipod i just a bigg mess, I've got 3 files to "We Are Pilots" so can't listen to the whole album properly. I wanted to change this tonight but I just found this topic so it will probably help me! I know some songs changed between those versions but I will check this later (as I'm tired blabla)
I don't have many songs because I removed the remixes songs, I don't very like remix. Don't blame me!
I've found naming the earlier versions with a v1.0 and v2.0 at the end helps keep the albums intact. No one blames you for not loving the remixes much. It's a personal preference thing.

Also, we have a "discography" topic that shows the track listings for the three versions. It may help you when you try to separate them?
Thank you Dear! Yes I saw this topic a while ago and it helped me! I deleted all my stuff and after that I put it again, changed some things and now everything is fixed! So I've got ... 47 songs! I thought I had more. But maybe because I removed all the remixes and V.1 / V.2 / V.3. Just got the songs once.