I use several flash or thumb drives, and I use them a lot. I have learned over time that it pays to treat these drives like other disk drives, meaning you need to worry about their health, and treat them to a defrag once in a while. If you have never done this, try it and see how badly (or not) fragmented it is, and defrag if you see lots of red.
Because flash drives are smaller, this takes very little time and protects your data and the health of your flash drive. I also recommend running a Check Disk (chkdsk) on these as well. They take a real beating and can develop problems just like a hard drive does. The chkdsk is only two phases and also is much quicker than a hard drive chkdsk.
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