I use the reader software to organize "collections." I use an sd card, and I have different collections on the sd card and the reader itself. I can tell from the collections menu screen which location houses a given collection (it will have an sd icon if itʻs on the card, otherwise it has different initials on the icon). When it has the list by date or alphabet, it also shows me which location houses that book.
So I have "solved" that problem by making collections in the sony reader software. You can also use Calibre (and some prefer it) to do the same thing, I believe.
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