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Yeah, saying no could potentially just sour things between you and your neighbours (even if you have the right to say no). I would want to be accommodating, but not taken for a mug. Take photos the morning before anything goes up, just in case. Best case, you get pleasantly surprised and you wouldn't know they had been there. Worst case, they're on the hook for some remedial works (worst worst case they don't follow through on their written agreement to fix stuff, in which case you get to sit on your high horse over them and/or take them to small claims, which they will lose).
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Have you asked about roped access for the roof work? We chose that on our tenement roof. Part of why I liked it was less chance of randoms trying to climb up the scaffolding and breaking into flats. Also it was comparable in price to the scaffolding option (slightly more cost but not much) and took less time to complete.
Scaffolders are a different breed and will be subbed in by the roofers. Accountability is key so I would ask for something in writing (or verbally, if you implicitly trust your neighbours) that any damage will be put right by hook or by crook. The scaffolders won't give a shit so either the neighbours themselves or their roofers will need to be responsible.