You will find out why I always advise new home buyers not to buy unless it has an NHBC warranty, which itself is far from perfect.
With Premier, you will have to pay an excess (from memory it is either £1000 or £1500.)
More than enough to re cover a flat roof.
But from what you have said, it might be more serious and involved.
I would advice t=you make a claim anyway, if for no other reason than to waste their time. At least you will find out what needs to be done and the cost. You can then get contractors in to do the remedials properly.