Ann,
I think things are getting confused here. Neither the Land Registry (now called the Property Registration Authority) nor the Registry of Deeds register the existance of buildings. They register the ownership of land. Your friend owns the land. She is the registered owner of the land. Therefore the second house is registered (assuming it's land reg title, on the same folio as the first house).
It is possible for your friend to separate the registration so that each house is on its own folio, but there is little point to doing this unless you want to sell the house, and I think this is why the solicitor said it would be costly & messy. Its unnecessary expense.
To be clear, the bank currently has a mortgage on both properties. Your friend gave the bank a charge over all the land. When she built the second house, she built it on land already charged to the bank.
If she now thinks the land is worth a lot more, then she can approach her existing bank and ask them to release the charge on one of the properties. Alternatively she can go to a new bank, get a mortgage sufficient to pay off the old bank, offering only one of the properties as security.
You will still have to get a map drawn up to clearly identify which property is being charged, so that you don't inadvertently mortgage both properties.
Any conveyancing solicitor will be able to help you with this.
Best of luck.
Kate.