You know, when I was stationed over in Germany (back during the Cold War), I remember hearing rumors (don't know if true or not) that all of the tunnels and key bridges were mined. So they could be blown up in the event of a Soviet invasion.
Don't know if that was true or not, but it would be terribly surprising if the British MoD didn't have some sort of contingency plan to do just what you suggest ("flood the tunnel") just in case...
Ever heard of “ADM” - Atomic Demolition Munitions?