Part of problematic configuration is removed after reboot when there is missing interface that was used in configuration.
For example. When you configure high availability and you use transition script and after that you change name of the script. After reboot high availability configuration is gone.
Would be nice to see some notification when you enter to configuration mode about this change in config.
admin@vyos01:~$ configure
[edit]
!!! Warning, there is a problem with high-availability configuration
Part of your configuration is inactive !!!
admin@vyos01#
Something like that maybe 