Hello, I am a solicitor with 20 years experience. I will try to help you with this.
You should go to the report on property from your solicitor at the time you purchased. This should make it very clear exactly what is included in your property. There will be a parcels clause in your purchase contact which will define the extent of your property. As a starting point you can check the title plan and office copy entries at the land registry (available online for a fee) which will show what the land registry thinks the position is. This is not definitive but it is a good place to start.
It would be unusual for your unadapted roof to belong to the upstairs neighbour. When did you move in?
Is there actually something built on top of your roof by the upstairs neighbour? Also is the freehold for the property a single freehold title for all the flats in the building?
OK thankyou. I think the position here is that you have the right to build using your planning permission. You should tell your neighbour that you intend to get on with the building and invite him to provide evidence of his claim. You should tell him that it is clear from the lease that you own the roof. As there is a joint freehold for the property he can not have an easement to use your roof.
You should give him a time limit to respond and tell him you will proceed after that time unless he provides sufficient evidence that he has any legal interest in the roof. Any right must proceed from his lease and from no other point (eg he can not have got any rights in these circumstances through prescription (ie long term use).