Well, I've had a go at following @compurandom's idea of only moving a few books/files at a time.
Well... so far so good.
I'm only moving over about 40 epubs at a time, and have been wi-fi syncing after each to make sure it's still working
Of course, I moved a lot of epubs (in stages) over a couple of hours , so I ended up with a corrupted database
But logging in and out of my Kobo account sorted that.
for all your help.