Something similar happened to me. Transferred books to Aura via Calibre, everything looked OK, little green ticks in the 'books on device' column and all that.

Disconnected, waited for it to process them, or shelve them, or whatever it does. Everything looked good.

Then when the Aura returned to the usual home screen, guess what... no books! I looked in the library just to make sure, and the only books in it were the icons for the non-downloaded ones I've bought from Kobo over the years.

So I plugged the Aura back in, connected it, and went back to Calibre, which - again - told me that the books were on the Aura.

So I disconnected it again.

And... guess what? The books had appeared right where they were supposed to be.

This has happened a couple of times; it's really quite weird.

The point to this, I suppose, is that I'm just saying that if your books are supposed to be on the Aura and don't seem to be, then don't panic immediately. Reconnect and disconnect again and see what happens rather than doing anything complicated and difficult first off.

If that doesn't work, then it's OK to panic.