From the discussion in the comments on your post I am still confused, but what I understand is that you're trying to:
Save a POST in a format similar to this:
array(
'Item' => array(
'id' => '3'
)
With:
$this->Item->SaveAll($this->request->data);
Your POST should contain a 'Action' key:
array(
'Item' => array(
'id' => '3'
),
'Action' => array(
'Action' => array()
)
When the "Action" key is set, Cake knows that it has to go "over" the relation and to it's magic.
Then it will delete.
I just tested this on a App that I'm developing and actually found it to be a bug. :D The problem
was that for the specific HATBM relation I had to use manually generated forms and thus when posting with nothing included the relation key was not set and the records, weren't deleted. I suppose that the Form Helper deals with this.
If you have a similar problem you can manage this in two different manners:
Put a hidden input with JavaScript
In the Controller check if the 'Action' key is set, and if not add it (as an empty array):
$this->request->data['Action']['Action'] = array();
This may be kind of intrusive, but It'll do the job.