Found Quarantine on old webinterface under configuration / antivirus scanner. Restoring everything from quarantine brought back cockpit functionality. I will investigate further but for now I have disabled quarantine, put unofficial signatures back to low, and will observe the next fullscan before activating quarantine again, problem solved.
Fortunately the old server manager is still there. I hope it will not be removed, as it is aparently rock-solid and helped me more than once 