It's the electronic records at the Land Registry which take precedence but you will get the physical deeds back.
Don't expect the lender to be particularly efficient when it comes to returning them though! I hope that your experiences are better than mine. I handed over a banker's draft (for over £30,000) to pay off my mortgage and declined the offer to store my deeds (for a fee). I waited for several months for the deeds to turn up. Eventually I got a recorded delivery letter from the Woolwich (as it then was). I opened it in the expectation that it would relate to the return of the deeds. I was stunned to find that it was a notice of intended repossession! They'd managed to mislay my payment and thought that I'd defaulted on the mortgage.
When I visited the local branch to get things sorted out, they eventually found my payment on their system but then asked me for another couple of hundred quid to cover the interest that had built up due to their error! It was only when I pointed out the proximity of their office to that of the local newspaper that they agreed to write off the interest.
It still took another month or two before I got the deeds but I then thought that everything was finally OK. More than a dozen years later, however, I tried to sell part of my garden to a neighbour, only to be told that I couldn't because the Land Registry records showed that the Woolwich still held a charge against the property! (I had great fun getting that sorted out because the Woolwich no longer existed!).
Good luck!
Chris