Oddly enough, that same exact thing happened to me with a new spare Glo I picked up yesterday. The books were definitely on the reader, yet the reader never showed them in the library. I tried logging out of the Kobo account on the reader, then it locked up a short time after and I had to do a soft reset (by just inserting a paperclip in the bottom hole). Once I got logged back into the account (had to go through the setup process again), the books I sideloaded were now visible on the reader. So try logging out and back in, and then the soft reset if that didn't do it.
Now I'm trying to figure out why books aren't being seen in the newly named "Collections" like on my older Glo (but I suspect it has to do with the name change from "My Shelves"). If it means setting up a different plugboard, not sure how that will work between the older Glo which I keep on firmware 2.4.0, and the new Glo that I thought I'd keep on the most current firmware just to see the changes (since I won't really be using it). And have to get rid of a mess of empty collections that syncing added back to the reader.
It only updated to firmware 3.3.0, but there's enough annoyances that I might just give in on the idea of watching new changes and putting 2.4.0 on it also. One really odd thing I noticed is the line spacing is different between firmwares. 3.3.0 claims to set the spacing down to 1.0, yet has more distance between lines than on the 2.4.0 firmware which could only be set manually to 1.225.
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