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Trying to go only through the top is possible but tricky - expect it to be a long job, and to have to unpick some stitches. On the bags that have the waterproof lining to the flap I tried to just sew through the cotton, on the grounds that it might be marginally more waterproof, but on the vintage bags with two layers of cotton I just went through both, which is much quicker and easier. You'll want to use a thimble and a fairly chunky needle - I've broken smaller ones in the past.
(I'm not sure I've ever ridden for any prolonged period of time in heavy enough rain to test whether the waterproofing would make a difference...)
Sewing patches onto a Carradice, blast it through both layers of the flap or try and only go through the top?