Follow standard upgrade procedures from 1.1.7 to 1.2.0-epa2 (add system image /mnt/vyos-1.2eta2.iso) with active configuration file. Upon reload, the entirety of the VPN section was not in the running config, but was present in /config/config.boot.

I attempted to load the configuration file and commit (load /config/config.boot) and got the following commit error:

commit
[ vpn ipsec logging log-modes all ]
must be one of the following: dmn, mgr, ike, chd, job, cfg, knl, net, asn, enc, lib, esp, tls, tnc, imc, imv, pts

[[vpn]] failed
Commit failed

Manually removing the following lines from /config/config.boot allowed for successful commit:

logging {
log-modes all
}