Thank you for the tip Heather, I tried to connect it to the the PC to transfer with the software and the reader froze. This was luckily a good thing since it forced me to hard reset the reader and all my books were there when it turned back on.
It just needs to be turned fully off (by holding the power button for a few seconds) then on again when you transfer books to the SD card without software. You can't create "collections" without the software though, which is a bit of a shame. I was hoping it would automatically create collections from the sub-folders I put them in. oh well, at least I can see my books now
Thanks again.