<fieldset class="nested">
   <legend>Ingredienti</legend>
   <ol id='ingredients'> 
    <%= render :partial => 'dummy_hidden_fields' %>

    <%= fields_for :quantities do |recipe_quantities| %>
    <li class="fields">
        <%= recipe_quantities.select :ingredient_id, options_from_collection_for_select(ingredients_for_select, :id, :name_unit, recipe_quantities.object.ingredient_id) %>
        
        ...
        
        <%#  fields_for will automatically generate a hidden field to store the ID of the record, so the following line is not necessary %>
        <%#= recipe_quantities.hidden_field_tag 'recipe[quantities_attributes][][id]', dq.id %>  
 

        <%# when you use a form element with the _destroy parameter, with a value that evaluates to true, you will destroy the associated model (eg. 1, ‘1’, true, or ‘true’) %>
        <%= recipe_quantities.hidden_field :_destroy, 0  %>
        <%= link_to_function "elimina", "remove_ingredient(this)", :class => 'btn btn-mini' %>       
    </li>   
    <% end %> 
</ol> 
<%= link_to_function "Add ingredient", "add_ingredient()" %>

<fieldset class="nested">
   <legend>Ingredienti</legend>
   <ol id='ingredients'> 
    <%= render :partial => 'dummy_hidden_fields' %>

    <%= fields_for :quantities do |recipe_quantities| %>
    <li class="fields">
        <%= recipe_quantities.select :ingredient_id, options_from_collection_for_select(ingredients_for_select, :id, :name_unit, recipe_quantities.object.ingredient_id) %>
        
        ...
        
        <%#  fields_for will automatically generate a hidden field to store the ID of the record, so the following line is not necessary %>
        <%#= recipe_quantities.hidden_field_tag 'recipe[quantities_attributes][][id]', dq.id %>  

        <%# when you use a form element with the _destroy parameter, with a value that evaluates to true, you will destroy the associated model (eg. 1, ‘1’, true, or ‘true’) %>
        <%= recipe_quantities.hidden_field :_destroy, value: 0 %>
        <%= link_to_function "elimina", "remove_ingredient(this)", :class => 'btn btn-mini' %>       
    </li>   
    <% end %> 
</ol> 
<%= link_to_function "Add ingredient", "add_ingredient()" %>

Instead of using a hidden li to add new ingredients, to use a template, like in this example (written in haml):

%h1 Edit Task Collection
= form_tag task_collection_update_path, :method => :put do
  %table#tasks
    %tr
      %th Name
      %th Priority
        - @tasks.each do |task|
      = fields_for 'tasks[]', task, :hidden_field_id => true do |task_form|
        = render :partial => 'task_form', :locals => {:task_form => task_form}

  = button_tag 'Save'

= button_tag "Add task", :type => :button, :id => :add_task

%script{:type => 'html/template', :id => 'task_form_template'}
  = fields_for 'tasks[]', Task.new, :index => 'NEW_RECORD', :hidden_field_id => true do |task_form| render(:partial => 'task_form', :locals => {:task_form => task_form}); end

:javascript
  $(function(){
    task_form = function(){ return $('#task_form_template').text().replace(/NEW_RECORD/g, new Date().getTime())}
    var add_task = function(){ $('#tasks').append(task_form()) }
    $('#add_task').on('click', add_task)
  })