What do you mean by "delete everything"? Do you mean only object nodes, or *all* nodes? You really, really should not delete everything! Although it should not cause a crash, the default scene setup is really meant to be built on and adjusted, Terragen needs most of those nodes to function correctly.
Even just the object nodes in the default scene need to be there for things to work normally and correctly.
That being said, I was not able to reproduce the issue. If you can give more specific instructions for how you cause the problem, we can see whether it is a real bug, or simply a misunderstanding of how to work with Terragen.