I spent the best part of 20 years, on and off, in negotiation with the Envronment Agency to get a huge area of flood plane, pools and ancient woodland transferred over to the Wildlife Trust as a nature reserve, Park Hall. It was mostly a failed flood alleviation scheme with woodland on the slopes up to the M6. We got longhorn cattle grazing it, there were loads of birds, amphibians, orchids, otters all right on the edge of Birmingham. We were working with the EA to move the canalised river tame back on to its old, winding course which would have vastly benefited widlife and helped address flooding downstream (a bit).
When HS2 was coming in initial discussion we looked at accepting a cutting through the ancient woodland and a line across the site in return for infrastructure improvements, land in compensation for what was lost and the river (which they have to move over anyway) restored to its original course. Not perfect but acceptable.
Plans changed, the promised compensation and investment in the site came under pressure from budget reductions. The site will now be used as a huge storage area during construction. HS2 'took possession' years ago and now it is unmanaged and waiting to be trashed.
I don't know how many similar stories are along the route.
http://www.bbcwildlife.org.uk/park-hall
Neil