I finally figured out what was going wrong on my Kobo Aura HD after I updated to 4.18.13737...
Looks like the new firmware "prioritizes" the content on the additional storage (SD card) - or maybe now sorts "most recent" based on most recently accessed? Thus, I was seeing the PDF's and image files I had saved onto it but which should be pretty much at the end of my list if it was based on file time-stamp.
If I remove the SD card, my book list looks as it should, with my most current ones at the top.
So... I guess for now I will just take the SD card out (good thing I don't have a HUGE library)... Not sure where to contact to add it as a bug for a future revision though. And of course it will likely only affect the older devices which have external SD slots (and only those users who don't use the SD slot as their primary storage will really see the symptoms I saw).
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