How do you enter your your hosts in /etc/hosts? With hostname.domain? Or only hostname? If you specify a .domainand it is the same you use for conditional forwarding pihole2 will likely send queries for the local domain to pihole1 and ignore/etc/hosts`.
How many host do you have (fixed, DHCP)? If there are just a few you might want to checkout the "Local DNS Record" function pihole v5.0 came with. You could specify local DNS records on one pi and share with the other by copying the custom.list between them. As pihole DHCP is deterministic your devices should always get the same IP from DHCP and therefore you wouldn't have to change the entries in "Local DNS Records".
For redundancy and availability in general see here: