The {author_sort}/{title} - {authors} change worked..ish. Before that there was a #myshelves entry which was trying to save everything into a myshelves epub file on the main memory which seemed to be causing trouble.
So now I can move books over, they go into the correct file system, but collections aren't working. The collection categories are on the device, the books have category data on them, but they're not going into any categories when they're sent over.
Still, a lot better than this time yesterday when it was an empty brick!