Isn't that the same problem with zip files? So if we're assuming that the compressed SQLite format will take up the same or less space as the zip file, wouldn't that mean that exactly the same mitigations work?
Yes the problem is ”fundamental” here as there is no filesystem guarantees. You basically upload the whole file after modifying it just like you would a zip. My point was that this is just as good to leave to the application and gain some better control over failure behavior/recovery.