Kindle devices have the ability to receive books via a special email address. Each kindle has a unique address ending in kindle.com. You can use Calibre to send the books via email to your kindle through your own email address. However, if the end goal is to bypass Amazon entirely, this method would not suffice.
Before sending any books to your kindle email ...
I have this issue as well
Fix that works for me:
I read somewhere that it could be an issue relating to low battery, but this morning it happened with 54% power.