He was only meant to go there once, and it's the only room connected to the outside.
Room 12 has a markedly different appearance to the rest of the castle: in particular, the unusually smooth walls and large block of azbantium. This is the 'final' room.
The castle is designed to get the Doctor to reveal the identity of the Hybrid. The designers thought he would only arrive in the trap room once, realise it’s impossible to escape, give up, and tell the secret. They almost certainly didn't anticipate the Doctor chipping away at the wall over billions of years. And if he’s only supposed to visit this room once, then there’s no need for the room to reset.
Also, note that this room connects to the outside world, and is apparently the only room to do so. So it makes sense for the rules to be a bit different here. It may even have been impossible for the designers to make this room reset every time, since it's connected to the outside and the outside can't be 'reset' in this way.
Much of this answer is copied from the excellent answer by @alexwlchan on another Stack Exchange.