What operating system are you using? Windows 7? Vista?
What version of doubleTwist on your PC? 3.2 or 4.0? I assume 4.0 since you are mentioned downgrading?
What device? What version of Android? Stock carrier ROM or custom ROM?
Are you using USB or AirSync?
Whenever you unselect something in the sync settings, that may trigger doubleTwist to remove it from your device if doubleTwist was used initially to sync it and no other sync selection reference the media file.
But if you did not unselect anything and doubleTwist Sync is removing files, please send us a debug package immediately after the sync and I will ask the QA/Dev team to investigate.
You can do this by holding down SHIFT while right-clicking on the doubleTwist icon and selecting "Send log files…".
Here's a short help page on how to send the debug package.http://www.doubletwist.com/help/question/doubletwist-sync-debug-mode/#E
Please include this support topic in the "Additional Information" section for reference.plus.google.com/u/0/117045529033446357900/posts/Tmvrej7Uz1b?cfem=1
Also, please include a short note on how you reproduced this problem.