I've got AA 1.5 and I'm assuming it's identical to 2.0 in this regard.
Here's how I do it:
* In Multitrack, right click on the wav you want to delete. You get a dropdown menu.
* Left click on Destroy Track, and then click Yes on the popup you get.
* Then go into Edit View, and click on File, and then Save As.
* Make sure that the Save As window is displaying the session you want (the one you're in in Multitrack).
* Right click and highlight the track you want to delete. You get a dropdown menu.
* Left click Delete, and then click Yes in the popup.
At this point, it's useful I find to go back into Multitrack and do two things:
* Click File and then Close Only Non-session Media. Then click on File and then Save Session.
At this point, the tracks you want should be completely deleted from the session. However, if you go into Windows Explorer and look inside the folder that contains your session, you'll see that the PK file for the deleted track still exists - the wav has been deleted, but for some reason the procedure I use doesn't delete the PK file. This doesn't affect the session in any way that I've ever found, but if you're obsessed with being tidy, you can delete the PK file for the deleted wav, cuz you don't need it any more. I usually just leave 'em though.