I've read on some other forums that people have had some problems when they add new files to the flash drive they are using for music. Some people have said that if they add new files to existing folders Sync won't see those new songs. Here is what I found works for me.

When unplugging the flash drive, have the stereo on, but playing radio, not MP3's. If you unplug the flash drive while Sync is playing from it, the drive may become corrupted. If the stereo is still on but playing radio, Sync will detect that the drive has been removed, so that when you plug it in again (also with the stereo on), it will take a look at your contents in case you have any new ones.

Here's one example where Sync doesn't notice a change. Let's say you discover that one of your songs has been mislabeled. Maybe it's got "rock" for genre and you want it to be "blues". If you plug the drive into your computer and fix it, then plug the drive back into the car, Sync probably won't take note of the change. If you change the filename, though, like adding a 2 at the end of the filename, it will cause Sync to disregard the original data because that exact file no longer exists. It will read in the data from the "new" file and everything will be fine. I'm not saying that this is the only way to do it, but it works for me.