It turns out that in /etc/commit/post-hooks.d/ there should exist a file named 00vyos-sync to take care of syncing to storage during commits.

However that file is deleted upon boot by vyos-router.

The file exists in the 'filesystem.squashfs` (verified through sudo find / -iname "00vyos-sync") but is deleted through the overlay filesystem during boot by vyos-router which makes it not visible when looking at /etc/commit/post-hooks.d/ (and therefor no syncing is done when commiting config changes).

The error is located at https://github.com/vyos/vyos-1x/blob/current/src/init/vyos-router#L222:

excluded="10vyatta-log-commit.pl 99vyos-user-postcommit-hooks"

The fix is that the above line should read:

excluded="00vyos-sync 10vyatta-log-commit.pl 99vyos-user-postcommit-hooks"