Not sure if helpful to anyone else.
After doing this I got an error in diagnosis "Ignoring duplicate dhcp-option 6"
I realised I already had
/etc/dnsmasq.d/99-second-DNS.conf
with
dhcp-option=option:dns-server,MYPIHOLEIP.
I deleted my 02-pihole-dhcp.conf and edited 99-second-DNS.conf to
dhcp-option=option:dns-server,MYPIHOLEIP,SecondaryDNSIP
There is no 02-pihole-dhcp.conf in Pi-hole v6.
It was used by Pi-hole v5.
Even when using Pi-hole v5, you should not delete that file, as it contains more than just that dhcp-option line, and it would be recreated by Pi-hole on certain interactions, resurfacing your conflict.