2 houses under one title

I am looking for some advice.  We are hoping to convert our garage into accommodation for relatives.

we applied for conversion into an annex but the planning application was refused.  The planners have recommended we apply again  as a separate dwelling.

we would like the 2 properties to stay as  one, as an annex would is this possible? What are the downsides of it being a separate dwelling and not an annex?

Emma - we register the general extent/boundaries so essentially the red outline on the title plan. That extent means all the land and building(s) within that red outline so whether the buildings change shape or even use has no impact 
The planning and 'use' aspects are all controlled by the local authority. The legal ownership and general boundaries are registered by us. Two very separate things