The way you do the delete it leaves everything after the dhcpv6-options in the config and only deletes the 56 which is not what you want. You want the whole node removed.
@ginko regardless of available workarounds, anything with a traceback should is a bug. Could you please verify if this behavior persists in the latest rolling release? If it does, please file a report at https://vyos.dev and include the full configuration along with the steps to reproduce the issue.
Happy to report the earlier reported issue didn’t re-appear on the latest nightly. I was able to delete dhcpv6-options from my config:
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admin@server:~$ show configuration commands | match dhcpv6
set interfaces pppoe pppoe0 dhcpv6-options pd 0 length '56'
admin@server:~$ conf
[edit]
admin@server# delete interfaces pppoe pppoe0 dhcpv6-options
[edit]
admin@server# commit
[edit]
admin@server#