I'm going to assume you are with UB given they seem to be trying to sort out the mess they have with missing deeds.
Unless you are intending on selling, the bank having the deeds at this point should make no difference to you. Whenever you want them back after the mortgage is settled, they will still have to cover the costs since they lost them. Make sure you have the current information in writing too.
Also it is normally standard practice to get compensated for time involved with this. I've only seen it where the bank covered extra solicitors costs during a sale, but it makes sense that they should cover your legal costs within reason too.