I recently deleted a number of books from my K3 because it seemed to be slowing down a lot. Still, even with less books now a lot of memory is being used--too much (I think) for only about 300 books.
If you deleted the old books by connecting the Kindle to your PC and deleting from there, it may be that Windows has created a recycle bin on your Kindle and put the books into it rather than truly deleting them - this could be the reason why the memory has not been freed.
The easiest way to fix this is to reconnect the Kindle and empty your recycle bin. If you want more control open your recycle bin, then click on the "original location" column to sort by it. Look for files on your Kindle's drive letter, select these and right click and delete.
.apnx is page numbers.. This is why sometimes page numbers don't show up right away.. They aren't actually in the book file, it is a separate file.
.ea is the "end action" file (that screen you get on the very last page of the book.. Do you want to share, rate.. Yada-yada)
.phl is the public highlights
.sa - I can't remember
Your books will still work perfectly fine if you delete any/all of these, but they may re-download themselves whenever you reconnect ~ sync. You just won't be able to use that particular "feature"
Useful list, thanks for this Heather! While trying (and failing) to google what .sa files are, I found this list which includes one extra one:
mbp = "associated information" (bookmarks, notes) for .azw books (presumably from Mobipocket still)
tan = associated information for Topaz books (presumably, "Topaz Annotation)
phl = presumably Popular Highlights
apnx = page numbers (presumably, Amazon Page Number something)
Personally if I delete a book I make sure I delete all the above files as well (ie anything with the same file name). I think if you delete from the home menu on the Kindle it deletes these as well.
If there are any "orphans" of these files left from previous books then delete them; I wouldn't delete them for books you are still reading though!
