Emptying USB drive?

Actually you are right.
The batch export mode using force overwrite by default.

In this case your question are quiet interesting.
Where the export processing finishing do you see (eg in file explorer) the 4.5GB new files?
You could try to format the drive then check again by exporting the data twice what happens. We had some strange behavior where the file system was damaged (partially) on the drive and some folder/file where not visible in the file explorer. That problem can be solved by formatting the drive. But I’m not sure you have a same problem or not.