Sorry, turns out I was drawing conclusions too soon. Changing read/unread through PRS+ for all 4300+ books worked fine, and the result was immediately clear in the book list. However, if I then shut down and start the reader again, it crashes on loading. So it's a no-go after all.
Rewriting the Sony's caching system is not feasible imho, but freeing up more mem should be. Or rather, it
feels like a possibility, since I have no idea how to actually do it