Spoke to the escalation team in Royal Mail and separately the Passport Office as well.
Guy in Royal Mail told me 99.99% of the time, it’s just a matter of slow updates and rarely the documents are missing.
When I checked the tracker for the Royal Mail, it is still not updated, but Passport Office have now confirmed they have received it.
I suggest calling them in the early mornings (Passport office and Royal mail), they are easier to get a hold of compared to later on in the day.