Hi there,
try to place signals to the sections which can’t be destroyed. This seems to change the ‘state’ of the track after which you can destroy it again.
If the section is to small, extend it again with extra track. Then place signals on this track.
This works for me every time. Play around with the signals, trying different locations if it doesn’t seem to work immediately.
I didn’t encounter an undestroyable tunnel yet, but perhaps this will work as well. You need to extend the entrance and/or exit then, as no signals can be placed inside the tunnels.
Also, read this http://www.train-fever.com/forums/topic/track-demo-bugs/.
Hope this helps!