I too can confirm that "Delete Hole" very rarely works properly on my projects. It seems like when I create a new project, it will work for a small amount of time in that project and then something happens that seems to turn it off. It just stops working and will not work again in that project. There are also times when the first time I go to use it in a project, it will not work. The problem is always that the selected area will delete, but the hole remains.
I have not yet been able to pin down what that something is to make this occur. As soon as I come across it, I'll post.
I'm sure I have seen threads regarding this issue but I have more pressing issues and have not followed this problem up. I will just work around it by sliding the tracks over the hole. I am assuming that "Delete Hole" works just fine for most users as it has not been a particularly active problem, at least that I can see.
I am also assuming that it is not my method, as sometimes it works and sometimes it doesn't. I have spent only a small amount of time trying to work out why this is happening, and although it's a small amount of time I believe I have been quite thorough, but have found no reason as to why this is occurring.
The most interesting/confusing/frustrating part of this issue is that "Delete Hole" often (but not all the time) seems to work ok when I create a new project, then seems to stop working after a small amount of time working with that project. Nothing specific seems to trigger the failure, I just go to use it and it will not work. As I said, the "delete" part will function fine, it's just that the hole remains.
I have many other issues with my projects and although I would like to get this one sorted, it is not particularly high on my list. It only slows down my workflow, not stop it or change it creatively.