Trade proceeded without agreed detail...

[catlad]

The installer asked me if they could take the hinges off to run the 0.8mm thick Zinc up the upstand. I called the rooflight manufacturer, who said ideally no, but as it was only 0.8mm it would be fine. So, I OK'd that to be done.

So when you agreed to them removing the hinges to waterproof the upstands why didn't they then replace the hinges?

 

[freddiemercurystwin]

Oh, that changes things. I appreciate that you did not fully understand the implications of removing the hinges but to be fair probably neither did the roofing contractor. I dare say they just did their usual standard kerb/upstand detail thinking any potential problems had been resolved between yourself and the rooflight manufacturer.
Legally I think you may be on the hook so hopefully a compromise can be found.

Probably a stupid question but can the rooflight frame/hinges be raised on a small secondary upstand with some kind of cover flashing to bridge the gap?

Yes you would expect whoever was managing the project to be hands on keeping an eye on proceedings, that's exactly the purpose of someone managing a project, an all overseeing eyes and ears, as soon as they said they wanted to take the hinges off your ears should have perked up.