It's hard to guess what might be happening without the log files.
However, I would delete the .qvds in the Qlik\Sense\Log folder and reload the apps to see if all relevant data appear.
Note that with Sense 2.0+ Monitoring Apps, you won't be able to load the majority of Sense 1.x logs because of a major change in the log files.
If removing the QVDs in the Sense\Log folder doesn't do the trick -- and the missing logs are 2.x -- then send over the Operations Monitor and License Monitor script logs from the most recent reload. (found in Sense\Log\Script)
I figured out a possible cause! I shut down the AWS instance the Qlik Sense server is installed on at 18:00 and I guess Qlik Sense Server does a job at 00:00 that archives the old logs. But since the instance is not running when that should happen it doesn't get done.Could that be the cause?