Interesting, it works fine here if I use the "Delete Special" menu and delete a hole.
Do you have MIDI data "in the hole" when you're deleting it ?.
If not, than that could be the problem ... that's the one thing I didn't test.
Otherwise, it may be a selection problem you're having.
I just tested this using a synth track with automation on the audio track (which as you point out is otherwise empty), and automation on BUSses too.
If I remember correctly it was buggy in X1.
X2 I think it worked OK, and X3 is definitely working fine here.
Just be careful to make sure you do have everything selected, I know I tripped up when first testing it out in X3.
I tested it twice just to make sure, and everything moved over, including all the automation on both tracks and busses.
Good luck.
Cheers - Cliff