Interest not registered with LANDregistry by Mortgage compan

[nhspartnershipmortgage]

My partner had a partnership mortgage which was sold as a perk for NHS workers. The impression was given that if the mortgage was paid off completely the flat would be owned by my partner but this turned out to be untrue and he has taken out a second partnership mortgage because there was a shortfall in the endowment to pay the mortgage off on completion. The mortgage company hasn't registered their ownership at the land registry. I just wondered what the implications of this were.