if I remote in via SSH and run the command everything works fine, but I am not sure why when deploying a new and when a failover happens (secondary router replaces the primary one). Even though I added the command to the start script, checking still shows the 99-conntrack.conf file.
I wonder if VRouter has a special way to set that parameter?
The VRouter is based in Alpine (which uses openrc) and I have experienced that, in some cases, the commands at the start script have problems to run. A workaround that worked for me in this cases is creating a script under the local service restart it. In that case you can have this as start script:
#!/bin/bash
cat >> /etc/local.d/custom_netfilter << EOF
#!/bin/bash
echo 262144 > /proc/sys/net/netfilter/nf_conntrack_max
EOF
chmod 744 /etc/local.d/custom_netfilter
service local restart