Thanks for the replies and thoughts everyone.
Quote:
Originally Posted by eschwartz
Books purchased at Amazon will have real page numbers added automatically. As long as the book has page numbers available, anyway. It is in documents/book-title.sdr/book-title.apnx although the first time you open the book (on a KT at least) it gets merged ino the annotations file...
Anyway, if you configure the device driver in calibre you can turn off (it's on by default) the auto-generation of a pseudo-apnx which guesstimates the pagenumbers. Also you can set it to accurate mode, or to derive page count from a custom column.
This works for both mobi and azw3. It is part of the send process, not conversion, so reconverting shouldn't make a difference? 
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You would think it wouldn't, but for whatever reason it seemed to in my case. Strange, eh?

And my Amazon purchased books that do have page numbers, but did previously, lost their page numbers until I reconverted and sent that one book file and then I noticed they actually appeared in the others as well then. Very strange behavior. It almost seems like sending that file forced some sort of change. Now all the books I have put on since have page numbers again.
Quote:
Originally Posted by NiLuJe
I vaguely remember people mentioning having to download (or send, or push, whatever, as long as it's done through an Amazon service) a book from Amazon to 'unlock' page numbers, which makes no sense whatsoever to me, because it's not a feature tied to the registration process AFAICT, and as eschwartz said, it's a single measly file sent by Calibre during the "Send To Device" process...
What I can say is that the format changed a bit with the advent of KF8, but I can't remember how Calibre decides which format to send (and I'm the one who did the KF8 tweaks for that... >_<").
EDIT: Yep, I went with what I thought was the safe way at the time (i.e. sending the new format w/ KF8 files, and the old format w/ Mobi6 files, instead of checking the target device model to make the decision [which, while doable, is annoyingly complex and potentially not 100% accurate on every platform...]).
TL;DR: So that might explain it, and the trick might be to – if it doesn't work with KF8 files at first – try sending a Mobi6 one to 'unbreak' everything  .
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Thanks for your reply. This seriously is what seemed to work for me. Sending that one mobi file seemed to literally unbreak everything as if by magic. Go figure.