Hi crypt0jan,
what Mattermost server version are you running?
I assume the process is running for some time, so while it is running, could you verify that the increased open files limit has been applied to this process? When it’s running, grep its PID and run cat /proc/<PID>/limits as well as lsof -p <PID> | wc -l to compare the values.
Maybe this one-liner helps with that:
echo "PID : Files-used/Soft-limit/Hard-Limit"; for pid in $(pidof mattermost); do printf "%-7d: %-10d/%-10d/%-10d\n" $pid $(lsof -p $pid | wc -l) $(awk "-F " '/^Max open files/ { print $4" "$5 }' /proc/$pid/limits); done