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All good points @Dugtheslug, @konastab01. And as you say @aggi, I wanted to air this dirty laundry to understand what the options were.
I think I mainly want to have a backed guarantee that the roof work they've done over our loft is good enough for many years. Especially where the new lead flashing on the chimney meets the existing tile and cement. If anything goes wrong, we it's not likely the insurance will cover poor workmanship, and we don't have any agreement with the contractor.
Psy-
I doubt you'll get anything worth anything from anyone going down the "official" route, other than some smiling and nodding.
If the job is signed off by the neighbour's building control officer then that's good enough for an insurance company/surveyor.
Are they a reputable company? Do they want to squander their rep by doing a shit job on something that is easy to do correctly?
I'd suggest talking to them openly and directly and asking them how they've weathered the roof, and express your worries to them.
Dugtheslug
What outcome do you want?
The current dormer wall to be knocked down and rebuilt?
Cash?
An inspection of the work on your side and a guarantee that if it fails you won't be liable for putting it right?
An apology?
What you want guides what approach you need to take.
Realistically though they could have got permission to build it to the party wall, as they have, so it's unlikely that anything is going to change about that.
Work on your side without permission is obviously a different matter but what do you want to resolve that beyond making good?