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Hampshire Nanny - Presumably you have more than calibre on the 128GB flash drive. How is performance of other applications on other data on the same drive.
FWIW : I have a library of ~40,000 books (20G), and another of ~8,000 books (600GB), mirrored to a USB3.0 spinning disk drive. Calibre performance on those libraries is faster than the same libraries on an internal SATA2.0 spinning disk drive . That said, the performance on the internal SATA 2.0 disk is more than good enough.
Have you checked the speed of the USB3.0 flash drive. Here is a review of some speed testers ==>>
6 Tools to Test Read and Write Speed of USB Flash Drives
Try copying the 400+ books to an empty library
without any existing custom columns and see how that goes. I have known composite columns to slow things down, but I hasten to add a) only on large libraries, and b) since Calibre 1.0 even those situations have gone away.
BR