Files are Disappearing

Ok this is confusing me beyond belief. I am converting avi files to mp4 and when I trash the old file the new one disappears too.

1.Oringinal file on desktop converting to mp4
2.Once completed the new and old file are on the desktop
3.Move new file to external HD
4.Trash both old and new file on desktop because it should be saved on the external.
5.Empty trash and the file on the external has disappeared. Sometimes replaced with a file thats just a bunch of numbers. Actually now its changing the file text document named season 4 that can't be opened.
6.Get angry.

I have no idea what I am doing wrong I can't see why it would delete it from the external. It does work however if once I move the file to the external then add it to iTunes, then trash everything it doesn't delete the file on the external.

 

Nevermind I think I figured it out I repaired my external drive and I am not seeing the problem anymore, plus it got rid of the unix files that I couldn't delete from the recycle bin.