I see that you're already trying to use the solution described here:
While not ideal, a work-around would be to automatically run your commands on boot. This page includes some methods of doing that:
Another possibility is that you're affected by the bug in the March 2017 update:
Another very thorough answer appears here:
16.10 fail to resolve DNS
I don't know enough about your precise circumstances to advise a particular one of these to try first, but hopefully one of them will work for you.
Update: Based on the knowledge that it's failing when the server reboots with a non-standard VPN client up, it's reasonable to assume that this VPN client could be modifying resolv.conf and removing some of the default entries in an attempt to avoid DNS leakage. I would recommend then making sure that your VPN client is disconnected before shutdown, and possibly still automatically resetting the resolv.conf after boot.
Alternatively, you could try adding a legitimate nameserver of your choice, such as
nameserver 184.108.40.206 to the file
/etc/resolvconf/resolv.conf.d/head, which might help. I am not sure if this will affect functionality of your VPN or not, or cause DNS leaking, so use it cautiously. Source: