This issue is quite similar to #103 , but instead of restarting systemd-networkd in step 6 in the reproduction explanation we experience the same problem by using netplan apply in a quite common Ubuntu 24.04 instance using systemd-networkd.
My precise GCE disk image is custom but it comes from a slight derivation of the ubuntu-minimal-2404-lts-amd64 GCP image family.

As far as I undestand the issue, this is what happens:

1. During boot, the Guest Agent inserts the Internal Network Load Balancer IP address in the local routes
2. cloud-init runs netplan apply which renders some changes to the systemd units representing the network interfaces
3. netplan apply run networkctl reconfigure 2 (to restart the main network interface using the new parameters)
4. Renewing the DHCP lease, the interface briefly loses the IP address and the Linux kernel deletes all the routes, including those that the Guest Agent inserted for using the Internal Network Load Balancer
5. The Guest Agent is already running, so the missing routes never get added again and the GCE instance remains offline from the perspective of TCP health check of the LB (sending a few bytes and expecting a given response).

Besides at the first boot when cloud-init runs, the machine at runtime experiences the same problem every time I use netplan apply.