I've sometimes loaded several hundred books in one session (mostly after I've gotten a new Kindle). If I leave the Kindle plugged in for the night (usually to a charger, sometimes to the laptop), it indexes a lot faster. Unplugged, indexing so many books can take a week. I don't remember anything being stuck indexing indefinitely, ever. All my Kindles have always managed to finish indexing at some point, sooner or later. You just have to be patient.
