Reports suggest that some Kindles delete all books sideloaded to a device after a certain period of time of having airplane mode has elapsed. Other reports suggest that changing an internal label on these books (EBOK to PDOC) may circumvent this problem.
Calibre still tags sideloaded books as EBOK, and it still doesn't offer a way to change it for AZW3 books, you have to tag them as PDOC manually.
If you're using KFX or MOBI, you might want to skip to the FAQ.
mu.update(asin, b'EBOK')
to...
mu.update(asin, b'PDOC')
You can use a metadata viewer to see if the book is actually a PDOC.
But I use MOBI/KFX. What do I do?
MOBI files by default are set to PDOC, I am not sure about this, but you can check this on Calibre Preferences > Output Options > MOBI.
For KFX books (you can convert books as KFX by installing KFX Output plugin), you can tell Calibre to always tag converted books as PDOC. (Calibre Preferences > Output Options > KFX Output > "Create personal document").
Is this method safe? Will something happen to my Kindle?
Yes it is safe, nothing bad will happen to your Kindle. There haven't been reports of PDOC tagged books being nuked so far, here is one report claiming their PDOC tags weren’t nuked.
But why not just use Send To Kindle? isn't that easier?
Maybe.