Oh, so it wasn't just me. I don't auto-update and I'm still running 5.4.4.19 (410) however, so it may have been an Android thing...
Anyway, I fiddled around with the folder locations in Settings. I set it to sd card (which i don't have) then reset to the original CC folder, and added this other folder that seems to have the same books, which i assume is where my reader keeps its data. By and by, it worked itself out.
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