Yes, "deeds" were the original sale documents used in the old unregistered system. The system of registering properties at the land registry replaced this and now the LR Official Copies are your evidence of title to prove you own the land. This is what you will need when you come to sell the land.
This is quite normal, nothing to worry about at all.
If the charge in favour of Natiowide is still registered against the property then you should contact them again and ask them to submit an Electronic Notification of Discharge to the LR so that the charge is removed.
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