Friend,
The settings that are made through CLI is sent by OLT to ONT through OMCI protocol. When ONT restarts, OLT sends the settings that were made via CLI to ONT.
For example,
If you configure VOICE services via CLI, and then change via WEB, when ONT restarts, OLT it will only send services configured via CLI and not configured via the web.
This behavior also happens with the Port Mapping settings that are made through the WEB interface.
I also recommend that you open a ticket with the TAC to analyze this behavior in more detail.
Tks