Funny, in my original question, I must confess to not spotting the spur line going to the waste recycling plant and was only focused on the remains of the old Glazebrook line. Somewhat surprisingly, during my drive into Manchester this morning, the plant fire was wall-to-wall on the news.
Some interesting responses to my original query. In particular, how some motorway num-nuts managed to damage the tunnel and close the through route forever.
I think an item of plant working above the tunnel discovered a hitherto unknown shaft, by falling down it. This damaged the lining, and the line was closed 'temporarily'. This line used to carry all the Yorkshire coal traffic (which had come via Woodhead) to Fidlers Ferry power station. That traffic had to be diverted via Guide Bridge and Stockport, then via the LNW Cheadle branch to regain the original route at Northenden Junction.
The closure became permanent sometime in 1981, when of course Woodhead had closed anyway.
I heard at the time that the damage wasn't necessarily terminal, but the tunnel was propped as a precaution and that effectively meant the end of the route.
The line stayed open from Woodley to serve the 'drops' at Portwood, but was later cut back further to serve a new facility replacing Portwood, to avoid the expense of a bridge over the new motorway.
There are some photo's of the tunnel as is it today on 28 Days Later, showing the propping, and more on flickr, including a few of the route when it was open, such as this one:
http://www.flickr.com/photos/deadmans_handle/6284057175/