I think I would go crazy if I'd used my e-reader as a way to keep track what I have read. That's why I use GoodReads. All my books are there, sorted by date, shelf, you name it.
I do have collections on my Kindles and put every new book in my To Read collection. When I'm finished I just move it to a different collection.
I only sideload my books so I have those same collections as folders on my computer and I update them about once a week (just move the books from my To Read folder to the right folder. I sort them by genre).
So if I need to reset one of my Kindles, I can easily load my books per folder onto my Kindle and then add them to the right collection manually.
So not really helping you with your problem I think, but just showing you a different way.
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