This issue is resolved in vCenter server version 6.7U3j and later, and 7.0 U1 and later where even if an older configuration file is present, it will be updated to the new format.
Workaround:
As a workaround the following process may be followed:
1. Remove all the huge log files under /var/log/vmware/vsan-health
2. Remove /etc/vmware-vsan-health/logger.conf
3. Restart vsan-health with: vmon-cli -r vsan-health