The battery probably got all used up indexing 1000 pdf files at one go.
Huge numbers of books slapped on it at once will consume massive amounts of battery power indexing those files (or trying
to index those files). Plus some of those 1000 books may be stuck indexing. Put the books on in smaller amounts and give the index process time to complete before adding more.
While no one will argue that a myriad of details (location, drm status, time, etc..) doesn't get logged to a file on the Kindle itself (nor will they argue its ability to communicate that logfile to Amazon if it wanted to) ... BUT! ... no one, to date, has ever caught a Kindle actually sending any
of that data back to Amazon yet. And many have tried.