You can replace it with a newer membrane.
You could cut the new felt so that you only replace the area that is damaged, just make sure to allow the minimum overlap (which I believe is 100mm on A1 protect)
What's on your roof? Slates or tiles? You could install vents near the bottom of the roof and if you make sure that the ridge is vented you should be good.
If you are doing the extension it would be worthwhile having the roof redone. Would save paying for scaffolding going up in the future etc.
Plus you would want your new extension to be properly ventilated.
Can you post a picture of the side of the window to show exactly which kind of flashing kit was used. You should be able to do it from opening the window.
It depends on a few things I suppose. I know in Edinburgh and some listed buildings I've worked on in central Scotland lead is required most of the time.
You can use a Ubbink vent and connect it up with a UB39 adapter.
This will keep your roof looking neat.
http://www.ubbink.co.uk/products/Roofing/Roof-vents-terminals/Slate/Vepac-Slate-Vents.aspx