I've done two backups since the update - one to a NAS and one to a USB drive hanging off my PC. No errors with the former, but two or three errors as you described in updating the backup files to the USB drive. Just restarted the backup each time and it carried on from where it failed and eventually completed successfully. No problems backing up new rips since the previous backup.

MC200, Twinstore, 808v6/ID41 -> DSP8000SE (+ SB Touch, Sony BDP-3300, SKYHD, legacy cassette player)
2nd system: MC200 analogue out, Linn LP12, SB3 -> Quad 34 -> M60 rosewood
F80 (Rubino Micallizzato)
F80 (Rosso Corsa)