Thanks @joe90, yes it is a very big potential stumbling block...
Figure I can solve going over the raised joints with adjustable height pedestals supporting the decking which can also accommodate for the current rain runoff slope of the existing roof, to create a nice new flat deck.
Here's some first sketch ideas in case anyone is interested...be good to hear peoples thoughts actually.
First is the simplest, basically just railings on all four sides (nicer railings than what's actually drawn)
The other two sketches continue the brick wall up on two sides with railings or planters on top and possibly a privacy screen included. Have to say, due to the costs, the first option might be the way I'd have to go. If I did get planning permission that is (and thats a big IF).
Lastly, the ladder/roof access hatch arrangement