Best practices to avoid missing content (multiple formats)

I just published a book on Amazon (and sales are taking off) as Kindle and paperback. I compiled it as .mobi and .docx.

A friend just emailed to tell me that entire chapters were missing from the Kindle version. Apparently this happened because I compiled for Word, which required making a bunch of changes to separators, then made some corrections adnd re-compiled for Kindle. Took me about ten tries of moving text around and changing separators to get everything to show up.

This is very frustrating. Are there best practices to avoid this problem?

Wearing my hat as Principal of Hague Publishing I always load a to-be published final formatted ebook to both my kindle, and kobo (checking the mobi and epub formatted books respectively). I also ensure that I try to load and flick through the epub using Calibre (epub), and the Kindle reader and Kindle Previewer on Windows (mobi), and to load the epub to both my android tablet and phone and check them there.

I don’t use Scrivener for creating the ebook so unfortunately I can’t help you with that, but the above is always good practice.