Yeah, tunneling can be bad news. There's also the issue of overly complex geometry when working with tunnels. But if you get a catastrophic level collapse, you can often recover. It seems to be associated with detaching objects after a rewind. I had my Grimmaulchkin level fall apart, but reloading it from just before the edit, it was safe. So basically, if it all goes to pieces, rewind to just before it falls apart, save it to a new slot, exit to Pod and then go back into editing the newly saved level. It should be intact and you can detach/delete the offending object without everything falling to bits. This works for me every time so I no longer fear the total level collapse as I used to. I keep an eye out for it, but it can be recovered as long as you don't save after it's fallen to bits.
Oh, and another thing to look for is if you have the editor paused and an object you move passes through existing geometry (as happend on Onooi for me). This means the catastrophic level collapses (CLC) has occured, and it's time to rewind to a point where everything was together, save, and try again.