Update (for if anyone is ever in this situation !):
After over an hour on hold I got through to someone on the phone and they said that both passports were waiting to be examined manually.
One of the passports had a query on it saying there were no lost passport details on it but the other didn’t have a query on it at all.
I asked them to add the lost/stolen reference to the passports (as it doesn’t look like it’s pulled through) and she said she added them on – so I guess it’s now just a waiting game