Flat Roof Side Window

I have just moved into a new house but have encountered the following problem, the side of the house has a garage with a flat roof and in my landing there is a side wooden side windows which is next to the flat roof. At some point the flat room must have been lifed to a height were the flashing is now over the window sill ! As the window is rotton I have therefore decided to replace with UPVC but the window company are not on the window being a part of the roof. So they have suggested that a 4 inch piece of timber is used to increase the height of the window but then attempt to flash the roof to the timber ! But they do not garantee that is will not leak !!!! Any one with a better idea for a flat roof flashing into a upvc window, would it be okay is use the 4inch wood or should it be brick !! As some stage (10years) I do hope to get rid of the flat roof !!!
Any ideas
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Gary Holt wrote:

I'm not surprised at them being uphappy. I don't see why they can't raise the window with a row of bricks, maybe they don't know how The guys that did my DG certainly were capable of re-laying a line of bricks under the new french window
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