I think my recommendation is going to be to leave each window where it is (like retro fit ones), install the lower flashing, then side flashing. I think if they carefully detail some Z metal/ drip cap flashing along the top and then install a flashing membrane above it, it should be good to go. So basically a properly detailed window flashing system without using the nailing flange as part of the system.

What do you all think.... any takers?