@ziggy9942:
It sounds like you are using FFF to update epub (which is what I recommend), but not updating the azw3 format afterward.
You can test that by manually converting from epub to azw3 and sending that format to your device again. You should then have all chapters.
I use a Kindle Voyage myself, and FFF has some settings to help. See highlighted:
One deletes the other (now outdated) formats on download, the other kicks off a convert automatically for each updated book. Note that you need to have your default convert-to-format set appropriately in calibre.