Please include all the requested information. We need to know which OS and which mono version (if Sonarr is not running on Windows).
There is nothing in Sonarr that would cause series to be removed automatically. Manually restoring an old database or having the DB stored in a location that is reset when the system is rebooted could cause issues.
I do see lots of errors in your logs in relation to connecting to indexers and metadata sources (thexem.de, skyhook, services).
It’s strange as it is working fine for couple hours and then series and calendar is again emptied, even without restarting computer. There are a lot of errors, but nothing I’ve googled has guide how to fix it.
We’ve seen similar things happen when anti-virus software starts changing files. Try disabling any anti-virus temporarily and see if the issue persists.