CGT on property sale where property is registered under two separate deeds

My wife and I bought a property in 1991. We bought the lower flat of a property that had been built in 1912 but split into upper and lower flats in 1973. We then bought the upper flat in 2002 and reinstated the whole house the following year. We are now selling the whole house but the titles deeds are still separate - the upper flat deed held in the main Registers of Scotland land register, the lower flat in the older sasine register. The house is recognised as a single property for council tax purposes and and has been our principal residence since 2003. Are any property CGT issues likely to arise when we sell or should we amalgamate the title deeds prior to sale?

Hi Gordon Simpson,
You will need to seek financial advice on the matter of amalgamting the deeds into one, as this is not a tax matter.
Please have a look at the helpsheet HS283 (HS283 Private Residence Relief (2024)) for private residence relief.  
There is also a calculator at Tax when you sell property, to help you work out your gain and the option to register for a capital gais tax account.  
Any gain from the disposal must be reported and paid within 60 days of the completion date.
Thank you.