There seems to be a big problem with configuration parsing in latest versions of VyOS. If you have both site-to-site vpn’s and an L2TP configuration the site-to-site VPN definitions in /etc/ipsec.conf and the secrets in /etc/ipsec.secrets will only contain the L2TP secret and definitions. I am assuming that this is from how the configuration is parsed and that the L2TP part is not appended to the file, but instead overwrites the config. The problem was not present in 1.2.1. In 1.2.4 the problem started with /etc/ipsec.secrets not containing the shared secrets for the site to site VPN’s. Starting from the currently available crux git-repos of 1.2.5 and the rolling 1.3 releases both the ipsec.conf and ipsec.secrets only contains the L2TP part.
There is also a small other cosmetic bug (or more specifically a fly?) in the file:
A few variables are misspelled with _flie instead of _file. This is consistent and should not really cause any problems more than being a cosmetic flaw.