Sorted my issue. It wasn't DNS (shock horror) as whenever I'd ping they'd resolve immediately and quickly fail to find the IP in ARP. My fix was to bin /etc/pihole/dhcp.leases and restart dns on pihole. Rebooted the pi and it got albeit the same IP as before but since then I have had no issues...
Sorry to get your hopes in with a reply to this thread on email but i have recently been having the same issues. Running an RT-AC88U on the latest Merlin. I am using a ubuntu VM for DNS and DHCP (pihole) and within the last few weeks I have been having the same issues as you. Only difference is...