I responded on stackoverflow, but I'll do here as well so that it is 
covered everywhere on the internet.

In my case I was doing something similar to what you were doing and was 
running into the same issue with the join table being deleted instead of 
destroyed.

I started looking through the code and I believe the documentation is just 
out of date.
[has_many_through_association](https://github.com/rails/rails/blob/master/activerecord/lib/active_record/associations/has_many_through_association.rb#L131)

All you need to do is add the dependent: :destroy to the has_many :through 
relationship.

    class User
      has_many :partnerships, dependent: :destroy
      has_many :partners, through: :partnerships, dependent: :destroy
    end

The pain I was dealing with was:
    
    user.partner_ids = [1,2,3]
    #creates the relationships
    user.partner_ids = []
    #was deleting the records from partnerships without callbacks.

The dependent: :destroy on the partners relationship fixed that.  Callbacks 
are now being run and things are good again.

Eric

On Monday, December 14, 2015 at 5:43:57 PM UTC-7, spike22 wrote:
>
> I've asked this on on Stack Overflow but didn't receive much of a response:
>
> The Rails 4 documentation says this regarding destroy callbacks on the 
> join model for a has_many :through relationship:
>
> collection=objects Replaces the collections content by deleting and 
> adding objects as appropriate. If the :through option is true callbacks in 
> the join models are triggered except destroy callbacks, since deletion is 
> direct.
>
> Thankfully it's documented at least, but I want to know why on earth this 
> is the case? It makes more sense to trigger destroy callbacks (or have the 
> option to) on a :through since these types of models can have destroy 
> callbacks and other associations.
>
> In my case I had a has_and_belongs_to_many relationship on the join 
> tables model off to another model. The records on that second join table 
> would never be deleted when the associated records on the first join table 
> were deleted. I resorted to this which feels hacky, and I have to repeat 
> myself on each side of the :through relationship:
>
> class SchoolsTemplate < ActiveRecord::Base
>
>   belongs_to :school
>   belongs_to :template
>
>   has_and_belongs_to_many :groups
>
> end
>
>
> class School < ActiveRecord::Base
>
>   has_many :schools_templates, dependent: :destroy
>   has_many :templates, through: :schools_templates, before_remove: 
> :remove_groups_school_templates
>
>   private
>   def remove_groups_school_templates(template)
>     schools_templates.where(template: template).first.groups.clear  end
>
> end
>
> There's a validation to 'ensure' uniqueness on the join tables records 
> between the two foreign keys, so that's why I can call first in the 
> callback.
>

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